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Experiment: The effect of gravitropism on the meristem and accelerating elongation zone of Col-0 and arf7arf19 roots

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-546

Gravitropism plays a role in the development of the root system. Upon gravistimulation, a complex response initiated in the root cap eventually triggers the gravitropic root curvature. Previous studies have demonstrated that gravity-induced lateral auxin transport can promote a differential growth response on opposite flanks of the elongation zone; cell elongation rate is reduced at the bottom side of the distal elongation zone, thus promoting the root to bend downwards. Auxin-response factors (ARFs), ARF7 and ARF19 are the major transcriptional regulators involved in root gravitropism (Okushima et al, 2005).The global transcriptomic analysis approach will allow us to construct and infer gene networks for the action of gravity. This will link the initial gravity signalling to downstream genes regulated by the ARF7/ARF19 pair.Two zones of Arabidopsis root will be considered in this experiment: zone 1 or meristem (from the root tip to the top of the lateral root cap-approx. 350 um) and zone 2 or accelerating elongation zone (from the top of the lateral root cap to the first visible root hair bulge-approx. 500 um). In order for statistical networks to be built, a time series of data is needed. This study has used 0, 15, 30, 60, 120, 240 and 480 minutes of gravity stimulation by 90° reorientation.

About the Experimenter

Name:Miss Ethel Mendocilla Sato
Head of Lab Name: Malcolm Bennett
Lab:
Address:Plant and Crop Sciences Division, Plant Sciences Building, School of Biosciences, University of Nottingham
Sutton Bonington Campus, College Road, Sutton Bonington, Nottinghamshire, LE12 5RD, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 07752718446

All of the data available in this website/database is free, and you are free to do whatever you please with it. If you intend to publish work based on any of this data, please acknowledge us, contact the experimenter above, and either acknowledge them or use them as co-authors in the work.

About this Experiment

Experiment Type: genetic_modification_design, time_series_design
Number of Slides:56
 
Experimental Parameters:
parameter timepoint
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Mendocilla Sato: The effect of gravitropism on the meristem and accelerating elongation zone of Col-0 and arf7arf19 roots

Slide: Mendocilla Sato_546-1_WT_0mins_Rep1_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-1_WT_0mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-1_WT_0mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.452003
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.106040
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.897620
Spike_AFFX-r2-Bs-dap_5_signal60.635147
NoiseAvg:2.78,Std:0.07,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.056543
#P13995
Spike_AFFX-r2-Bs-phe_M_signal34.038479
Corner-Avg:7604,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal79.265038
Spike_AFFX-r2-Ec-bioB_3_signal59.816437
Spike_AFFX-r2-Bs-lys_M_signal18.228834
Spike_AFFX-r2-P1-cre_3_signal3635.108398
Spike_AFFX-r2-Bs-lys_3-5-ratio1.280089
Spike_AFFX-r2-Bs-dap_M_signal126.683388
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.849986
Spike_AFFX-r2-Ec-bioB_avg-signal68.573471
Spike_AFFX-r2-Bs-thr_avg-signal45.583759
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal777.492554
Spike_AFFX-r2-Bs-phe_5_signal21.528963
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1027.746704
RawQ2.568001
Spike_AFFX-r2-Bs-lys_5_signal19.028433
Signal(A)3.275382
%A37.023235
Signal(All)145.214294
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal247.226395
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.524197
Spike_AFFX-r2-Ec-bioD_avg-signal902.619629
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.354668
Spike_AFFX-r2-Bs-lys_avg-signal20.538450
Spike_AFFX-r2-P1-cre_avg-signal3460.853760
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.622096
Spike_AFFX-r2-Bs-thr_3_signal62.860840
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.363878
Spike_AFFX-r2-Bs-dap_3_signal177.595505
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.321873
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal249.874237
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.358080
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.989403
Spike_AFFX-r2-Bs-thr_M_signal51.833889
Signal(P)234.317825
Spike_AFFX-r2-Bs-phe_3-5-ratio0.953330
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4792,Count:9
Spike_AFFX-r2-P1-cre_5_signal3286.599121
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8445
Signal(M)14.592824
BackgroundAvg:63.52,Std:0.38,Min:62.7,Max:64.5
Spike_AFFX-r2-Ec-bioC_avg-signal248.550323
Spike_AFFX-r2-Bs-dap_avg-signal121.638023
Spike_AFFX-r2-Bs-dap_3-5-ratio2.928920
Spike_AFFX-r2-Ec-bioB_5_signal66.638931
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.452003
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-2_WT_15mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-2_WT_15mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-2_WT_15mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.585367
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.995516
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.001567
Spike_AFFX-r2-Bs-dap_5_signal57.188553
NoiseAvg:2.78,Std:0.10,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.840302
#P13474
Spike_AFFX-r2-Bs-phe_M_signal15.021028
Corner-Avg:6480,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.979530
Spike_AFFX-r2-Ec-bioB_3_signal60.724674
Spike_AFFX-r2-Bs-lys_M_signal8.335648
Spike_AFFX-r2-P1-cre_3_signal3511.426270
Spike_AFFX-r2-Bs-lys_3-5-ratio2.152395
Spike_AFFX-r2-Bs-dap_M_signal83.514343
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.462076
Spike_AFFX-r2-Ec-bioB_avg-signal66.444618
Spike_AFFX-r2-Bs-thr_avg-signal50.370697
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal666.294495
Spike_AFFX-r2-Bs-phe_5_signal30.527563
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1112.486084
RawQ2.519260
Spike_AFFX-r2-Bs-lys_5_signal10.840147
Signal(A)4.417734
%A39.013592
Signal(All)148.682785
Corner+Avg:101,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal266.964478
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.046730
Spike_AFFX-r2-Ec-bioD_avg-signal889.390259
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.070583
Spike_AFFX-r2-Bs-lys_avg-signal14.169360
Spike_AFFX-r2-P1-cre_avg-signal3519.334961
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.915826
Spike_AFFX-r2-Bs-thr_3_signal86.520935
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.865107
Spike_AFFX-r2-Bs-dap_3_signal148.015808
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.669661
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal226.073044
#M437
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.332283
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.180877
Spike_AFFX-r2-Bs-thr_M_signal48.750851
Signal(P)248.247940
Spike_AFFX-r2-Bs-phe_3-5-ratio0.754948
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4491,Count:9
Spike_AFFX-r2-P1-cre_5_signal3527.243652
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8899
Signal(M)16.586283
BackgroundAvg:65.56,Std:0.27,Min:64.8,Max:66.6
Spike_AFFX-r2-Ec-bioC_avg-signal246.518768
Spike_AFFX-r2-Bs-dap_avg-signal96.239563
Spike_AFFX-r2-Bs-dap_3-5-ratio2.588207
Spike_AFFX-r2-Ec-bioB_5_signal60.629654
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.585367
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-3_WT_30mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-3_WT_30mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-3_WT_30mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.594754
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.130167
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.918473
Spike_AFFX-r2-Bs-dap_5_signal64.917381
NoiseAvg:2.35,Std:0.10,Min:2.1,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.046597
#P13853
Spike_AFFX-r2-Bs-phe_M_signal27.869175
Corner-Avg:7277,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal116.166161
Spike_AFFX-r2-Ec-bioB_3_signal74.596169
Spike_AFFX-r2-Bs-lys_M_signal19.438166
Spike_AFFX-r2-P1-cre_3_signal4317.908203
Spike_AFFX-r2-Bs-lys_3-5-ratio1.756880
Spike_AFFX-r2-Bs-dap_M_signal104.199043
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.671195
Spike_AFFX-r2-Ec-bioB_avg-signal90.659966
Spike_AFFX-r2-Bs-thr_avg-signal44.702358
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal829.244812
Spike_AFFX-r2-Bs-phe_5_signal28.395113
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1210.533813
RawQ2.238538
Spike_AFFX-r2-Bs-lys_5_signal15.841132
Signal(A)3.585912
%A37.597546
Signal(All)147.693390
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal349.501556
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.656813
Spike_AFFX-r2-Ec-bioD_avg-signal1019.889282
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.732136
Spike_AFFX-r2-Bs-lys_avg-signal21.036755
Spike_AFFX-r2-P1-cre_avg-signal4069.250977
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.670320
Spike_AFFX-r2-Bs-thr_3_signal58.890759
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal28.307032
Spike_AFFX-r2-Bs-dap_3_signal166.940643
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.459803
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal295.012634
#M381
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.830965
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.184700
Spike_AFFX-r2-Bs-thr_M_signal53.169712
Signal(P)240.573990
Spike_AFFX-r2-Bs-phe_3-5-ratio1.009216
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5237,Count:9
Spike_AFFX-r2-P1-cre_5_signal3820.593994
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8576
Signal(M)14.335767
BackgroundAvg:57.16,Std:0.57,Min:56.0,Max:58.6
Spike_AFFX-r2-Ec-bioC_avg-signal322.257080
Spike_AFFX-r2-Bs-dap_avg-signal112.019020
Spike_AFFX-r2-Bs-dap_3-5-ratio2.571586
Spike_AFFX-r2-Ec-bioB_5_signal81.217560
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.594754
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-4_WT_60mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-4_WT_60mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-4_WT_60mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.566956
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.170667
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.867464
Spike_AFFX-r2-Bs-dap_5_signal66.394531
NoiseAvg:2.55,Std:0.08,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.695211
#P13682
Spike_AFFX-r2-Bs-phe_M_signal19.009916
Corner-Avg:7747,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.237991
Spike_AFFX-r2-Ec-bioB_3_signal68.263779
Spike_AFFX-r2-Bs-lys_M_signal15.766417
Spike_AFFX-r2-P1-cre_3_signal4871.890137
Spike_AFFX-r2-Bs-lys_3-5-ratio2.753458
Spike_AFFX-r2-Bs-dap_M_signal106.545052
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.315943
Spike_AFFX-r2-Ec-bioB_avg-signal78.398438
Spike_AFFX-r2-Bs-thr_avg-signal40.166077
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal811.209961
Spike_AFFX-r2-Bs-phe_5_signal25.252287
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1119.925659
RawQ2.388425
Spike_AFFX-r2-Bs-lys_5_signal12.878845
Signal(A)3.798352
%A38.263920
Signal(All)152.340866
Corner+Avg:101,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal325.261627
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.763836
Spike_AFFX-r2-Ec-bioD_avg-signal965.567810
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.982464
Spike_AFFX-r2-Bs-lys_avg-signal21.368874
Spike_AFFX-r2-P1-cre_avg-signal4516.762695
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.753617
Spike_AFFX-r2-Bs-thr_3_signal55.360371
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.675346
Spike_AFFX-r2-Bs-dap_3_signal165.209885
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.380562
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal264.376709
#M400
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.461361
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.230296
Spike_AFFX-r2-Bs-thr_M_signal48.442646
Signal(P)251.115860
Spike_AFFX-r2-Bs-phe_3-5-ratio1.059858
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5506,Count:9
Spike_AFFX-r2-P1-cre_5_signal4161.634766
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8728
Signal(M)14.939301
BackgroundAvg:61.06,Std:0.34,Min:60.3,Max:61.9
Spike_AFFX-r2-Ec-bioC_avg-signal294.819153
Spike_AFFX-r2-Bs-dap_avg-signal112.716492
Spike_AFFX-r2-Bs-dap_3-5-ratio2.488306
Spike_AFFX-r2-Ec-bioB_5_signal78.693535
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.566956
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-5_WT_120mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-5_WT_120mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-5_WT_120mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.613237
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.193363
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.838257
Spike_AFFX-r2-Bs-dap_5_signal83.909805
NoiseAvg:2.45,Std:0.09,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.496029
#P13596
Spike_AFFX-r2-Bs-phe_M_signal30.791559
Corner-Avg:7032,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.557007
Spike_AFFX-r2-Ec-bioB_3_signal65.630753
Spike_AFFX-r2-Bs-lys_M_signal15.224895
Spike_AFFX-r2-P1-cre_3_signal5029.128906
Spike_AFFX-r2-Bs-lys_3-5-ratio1.313738
Spike_AFFX-r2-Bs-dap_M_signal162.242676
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.574411
Spike_AFFX-r2-Ec-bioB_avg-signal77.827370
Spike_AFFX-r2-Bs-thr_avg-signal49.306835
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal770.623169
Spike_AFFX-r2-Bs-phe_5_signal23.540041
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1041.900146
RawQ2.261301
Spike_AFFX-r2-Bs-lys_5_signal17.445095
Signal(A)3.825527
%A38.614643
Signal(All)151.240677
Corner+Avg:99,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal309.821259
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.613647
Spike_AFFX-r2-Ec-bioD_avg-signal906.261658
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.605434
Spike_AFFX-r2-Bs-lys_avg-signal18.529423
Spike_AFFX-r2-P1-cre_avg-signal4621.688477
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.779921
Spike_AFFX-r2-Bs-thr_3_signal60.488438
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal29.315081
Spike_AFFX-r2-Bs-dap_3_signal201.455811
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.352023
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal267.359161
#M406
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.918280
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.158820
Spike_AFFX-r2-Bs-thr_M_signal63.936039
Signal(P)250.828262
Spike_AFFX-r2-Bs-phe_3-5-ratio1.427935
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5161,Count:9
Spike_AFFX-r2-P1-cre_5_signal4214.247559
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8808
Signal(M)14.393167
BackgroundAvg:60.87,Std:0.45,Min:60.0,Max:62.3
Spike_AFFX-r2-Ec-bioC_avg-signal288.590210
Spike_AFFX-r2-Bs-dap_avg-signal149.202759
Spike_AFFX-r2-Bs-dap_3-5-ratio2.400861
Spike_AFFX-r2-Ec-bioB_5_signal78.294342
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.613237
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-6_WT_240mins_Rep1_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-6_WT_240mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-6_WT_240mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.704233
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.192415
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.848835
Spike_AFFX-r2-Bs-dap_5_signal79.838615
NoiseAvg:2.54,Std:0.10,Min:2.4,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.595484
#P13408
Spike_AFFX-r2-Bs-phe_M_signal31.100676
Corner-Avg:6050,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.756874
Spike_AFFX-r2-Ec-bioB_3_signal57.893208
Spike_AFFX-r2-Bs-lys_M_signal13.554680
Spike_AFFX-r2-P1-cre_3_signal4256.662598
Spike_AFFX-r2-Bs-lys_3-5-ratio2.273630
Spike_AFFX-r2-Bs-dap_M_signal138.297501
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.481148
Spike_AFFX-r2-Ec-bioB_avg-signal69.951057
Spike_AFFX-r2-Bs-thr_avg-signal71.458122
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal665.489624
Spike_AFFX-r2-Bs-phe_5_signal32.167683
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1005.018616
RawQ2.405716
Spike_AFFX-r2-Bs-lys_5_signal14.760524
Signal(A)4.676540
%A39.465145
Signal(All)149.149094
Corner+Avg:87,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal336.825836
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.629356
Spike_AFFX-r2-Ec-bioD_avg-signal835.254150
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.781235
Spike_AFFX-r2-Bs-lys_avg-signal20.625059
Spike_AFFX-r2-P1-cre_avg-signal3913.222900
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.753617
Spike_AFFX-r2-Bs-thr_3_signal99.545128
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal33.299240
Spike_AFFX-r2-Bs-dap_3_signal211.607605
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.510194
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal277.881592
#M400
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.559971
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.212120
Spike_AFFX-r2-Bs-thr_M_signal86.233734
Signal(P)250.068237
Spike_AFFX-r2-Bs-phe_3-5-ratio1.138700
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4299,Count:9
Spike_AFFX-r2-P1-cre_5_signal3569.783203
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9002
Signal(M)17.694138
BackgroundAvg:63.33,Std:0.29,Min:62.4,Max:64.2
Spike_AFFX-r2-Ec-bioC_avg-signal307.353699
Spike_AFFX-r2-Bs-dap_avg-signal143.247910
Spike_AFFX-r2-Bs-dap_3-5-ratio2.650442
Spike_AFFX-r2-Ec-bioB_5_signal68.203094
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.704233
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-7_WT_480mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-7_WT_480mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-7_WT_480mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.66353
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.038190
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.822023
Spike_AFFX-r2-Bs-dap_5_signal44.450806
NoiseAvg:2.67,Std:0.10,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.394636
#P13217
Spike_AFFX-r2-Bs-phe_M_signal15.541645
Corner-Avg:5290,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal78.004814
Spike_AFFX-r2-Ec-bioB_3_signal42.727688
Spike_AFFX-r2-Bs-lys_M_signal11.641356
Spike_AFFX-r2-P1-cre_3_signal3127.959717
Spike_AFFX-r2-Bs-lys_3-5-ratio1.238303
Spike_AFFX-r2-Bs-dap_M_signal101.518250
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.964511
Spike_AFFX-r2-Ec-bioB_avg-signal57.570393
Spike_AFFX-r2-Bs-thr_avg-signal55.986332
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal586.665100
Spike_AFFX-r2-Bs-phe_5_signal12.296206
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal846.772949
RawQ2.514772
Spike_AFFX-r2-Bs-lys_5_signal9.972030
Signal(A)4.547513
%A40.249889
Signal(All)149.375702
Corner+Avg:82,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal253.389282
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.359354
Spike_AFFX-r2-Ec-bioD_avg-signal716.718994
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.943886
Spike_AFFX-r2-Bs-lys_avg-signal11.320592
Spike_AFFX-r2-P1-cre_avg-signal3070.428223
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.806225
Spike_AFFX-r2-Bs-thr_3_signal91.320374
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal16.065737
Spike_AFFX-r2-Bs-dap_3_signal163.324097
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.443367
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal231.182648
#M412
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal12.348391
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.096057
Spike_AFFX-r2-Bs-thr_M_signal58.243996
Signal(P)254.134140
Spike_AFFX-r2-Bs-phe_3-5-ratio1.655743
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3407,Count:9
Spike_AFFX-r2-P1-cre_5_signal3012.896973
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9181
Signal(M)16.063622
BackgroundAvg:64.16,Std:0.40,Min:62.5,Max:65.1
Spike_AFFX-r2-Ec-bioC_avg-signal242.285965
Spike_AFFX-r2-Bs-dap_avg-signal103.097717
Spike_AFFX-r2-Bs-dap_3-5-ratio3.674266
Spike_AFFX-r2-Ec-bioB_5_signal51.978680
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.663530
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-8_WT_0mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-8_WT_0mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-8_WT_0mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.686543
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.881329
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.094040
Spike_AFFX-r2-Bs-dap_5_signal63.512890
NoiseAvg:2.60,Std:0.05,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.872786
#P13466
Spike_AFFX-r2-Bs-phe_M_signal26.780203
Corner-Avg:6779,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal87.735748
Spike_AFFX-r2-Ec-bioB_3_signal68.273880
Spike_AFFX-r2-Bs-lys_M_signal11.023443
Spike_AFFX-r2-P1-cre_3_signal3300.815674
Spike_AFFX-r2-Bs-lys_3-5-ratio1.088107
Spike_AFFX-r2-Bs-dap_M_signal104.659012
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.877167
Spike_AFFX-r2-Ec-bioB_avg-signal72.804977
Spike_AFFX-r2-Bs-thr_avg-signal51.977081
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal629.498901
Spike_AFFX-r2-Bs-phe_5_signal22.622152
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal966.627563
RawQ2.420913
Spike_AFFX-r2-Bs-lys_5_signal15.439407
Signal(A)4.631359
%A39.123192
Signal(All)149.833755
Corner+Avg:89,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal314.794800
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.159655
Spike_AFFX-r2-Ec-bioD_avg-signal798.063232
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.035511
Spike_AFFX-r2-Bs-lys_avg-signal14.420857
Spike_AFFX-r2-P1-cre_avg-signal3523.042969
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.841298
Spike_AFFX-r2-Bs-thr_3_signal80.927269
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal24.187338
Spike_AFFX-r2-Bs-dap_3_signal135.779388
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.535551
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.280792
#M420
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.799723
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.315587
Spike_AFFX-r2-Bs-thr_M_signal54.131184
Signal(P)250.202911
Spike_AFFX-r2-Bs-phe_3-5-ratio1.023760
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4730,Count:9
Spike_AFFX-r2-P1-cre_5_signal3745.270020
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8924
Signal(M)17.012011
BackgroundAvg:63.34,Std:0.33,Min:62.4,Max:64.2
Spike_AFFX-r2-Ec-bioC_avg-signal277.037781
Spike_AFFX-r2-Bs-dap_avg-signal101.317101
Spike_AFFX-r2-Bs-dap_3-5-ratio2.137824
Spike_AFFX-r2-Ec-bioB_5_signal62.405308
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.686543
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-9_WT_15mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-9_WT_15mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-9_WT_15mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.558928
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.101484
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.688522
Spike_AFFX-r2-Bs-dap_5_signal52.011284
NoiseAvg:2.65,Std:0.06,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.790071
#P13573
Spike_AFFX-r2-Bs-phe_M_signal16.990816
Corner-Avg:6485,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.058586
Spike_AFFX-r2-Ec-bioB_3_signal57.683403
Spike_AFFX-r2-Bs-lys_M_signal7.416835
Spike_AFFX-r2-P1-cre_3_signal3872.408447
Spike_AFFX-r2-Bs-lys_3-5-ratio1.503401
Spike_AFFX-r2-Bs-dap_M_signal91.790977
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.121789
Spike_AFFX-r2-Ec-bioB_avg-signal76.840187
Spike_AFFX-r2-Bs-thr_avg-signal48.587158
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal729.574524
Spike_AFFX-r2-Bs-phe_5_signal22.000874
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1143.923828
RawQ2.356636
Spike_AFFX-r2-Bs-lys_5_signal13.436035
Signal(A)4.023225
%A38.798771
Signal(All)148.023605
Corner+Avg:84,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal296.139893
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.200390
Spike_AFFX-r2-Ec-bioD_avg-signal936.749146
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.504604
Spike_AFFX-r2-Bs-lys_avg-signal13.684208
Spike_AFFX-r2-P1-cre_avg-signal3694.017822
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.696624
Spike_AFFX-r2-Bs-thr_3_signal71.145798
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.397360
Spike_AFFX-r2-Bs-dap_3_signal153.999146
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.567933
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal272.248993
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.199753
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.087754
Spike_AFFX-r2-Bs-thr_M_signal51.825611
Signal(P)245.691544
Spike_AFFX-r2-Bs-phe_3-5-ratio1.145427
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4869,Count:9
Spike_AFFX-r2-P1-cre_5_signal3515.627197
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8850
Signal(M)15.611746
BackgroundAvg:82.96,Std:0.36,Min:82.2,Max:83.9
Spike_AFFX-r2-Ec-bioC_avg-signal284.194458
Spike_AFFX-r2-Bs-dap_avg-signal99.267143
Spike_AFFX-r2-Bs-dap_3-5-ratio2.960880
Spike_AFFX-r2-Ec-bioB_5_signal83.778564
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.558928
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-10_WT_30mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-10_WT_30mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-10_WT_30mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.677839
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.966289
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.880910
Spike_AFFX-r2-Bs-dap_5_signal55.460011
NoiseAvg:2.48,Std:0.05,Min:2.3,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.598463
#P13466
Spike_AFFX-r2-Bs-phe_M_signal23.547014
Corner-Avg:5968,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.122841
Spike_AFFX-r2-Ec-bioB_3_signal64.333992
Spike_AFFX-r2-Bs-lys_M_signal13.641378
Spike_AFFX-r2-P1-cre_3_signal3367.932617
Spike_AFFX-r2-Bs-lys_3-5-ratio1.689635
Spike_AFFX-r2-Bs-dap_M_signal88.371399
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.844881
Spike_AFFX-r2-Ec-bioB_avg-signal76.162697
Spike_AFFX-r2-Bs-thr_avg-signal50.741398
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal606.625854
Spike_AFFX-r2-Bs-phe_5_signal14.786816
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1008.813782
RawQ2.240919
Spike_AFFX-r2-Bs-lys_5_signal16.375589
Signal(A)4.860261
%A39.219639
Signal(All)147.961990
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal281.063690
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.886333
Spike_AFFX-r2-Ec-bioD_avg-signal807.719849
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.035511
Spike_AFFX-r2-Bs-lys_avg-signal19.228579
Spike_AFFX-r2-P1-cre_avg-signal3426.681641
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.744849
Spike_AFFX-r2-Bs-thr_3_signal69.979706
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.740057
Spike_AFFX-r2-Bs-dap_3_signal146.459305
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.662992
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.360596
#M398
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.668768
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.145513
Spike_AFFX-r2-Bs-thr_M_signal57.646023
Signal(P)246.877594
Spike_AFFX-r2-Bs-phe_3-5-ratio2.224031
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4630,Count:9
Spike_AFFX-r2-P1-cre_5_signal3485.430908
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8946
Signal(M)17.787228
BackgroundAvg:82.14,Std:0.35,Min:81.5,Max:83.5
Spike_AFFX-r2-Ec-bioC_avg-signal263.212158
Spike_AFFX-r2-Bs-dap_avg-signal96.763573
Spike_AFFX-r2-Bs-dap_3-5-ratio2.640809
Spike_AFFX-r2-Ec-bioB_5_signal73.031273
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.677839
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-11_WT_60mins_Rep2_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-11_WT_60mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-11_WT_60mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.507267
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.110909
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.724292
Spike_AFFX-r2-Bs-dap_5_signal46.978760
NoiseAvg:2.69,Std:0.07,Min:2.5,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.648609
#P13692
Spike_AFFX-r2-Bs-phe_M_signal19.624918
Corner-Avg:6746,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.786430
Spike_AFFX-r2-Ec-bioB_3_signal48.742035
Spike_AFFX-r2-Bs-lys_M_signal9.592906
Spike_AFFX-r2-P1-cre_3_signal3667.526611
Spike_AFFX-r2-Bs-lys_3-5-ratio1.022737
Spike_AFFX-r2-Bs-dap_M_signal89.319038
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.476601
Spike_AFFX-r2-Ec-bioB_avg-signal67.608192
Spike_AFFX-r2-Bs-thr_avg-signal43.785091
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal647.745117
Spike_AFFX-r2-Bs-phe_5_signal24.759027
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1021.714172
RawQ2.509863
Spike_AFFX-r2-Bs-lys_5_signal14.938437
Signal(A)3.829722
%A38.430511
Signal(All)147.937531
Corner+Avg:91,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal266.329620
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.242048
Spike_AFFX-r2-Ec-bioD_avg-signal834.729614
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.026306
Spike_AFFX-r2-Bs-lys_avg-signal13.269814
Spike_AFFX-r2-P1-cre_avg-signal3484.451172
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.543183
Spike_AFFX-r2-Bs-thr_3_signal71.786980
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.208664
Spike_AFFX-r2-Bs-dap_3_signal141.002060
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.577340
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal253.541916
#M352
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.278096
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.050436
Spike_AFFX-r2-Bs-thr_M_signal38.919685
Signal(P)243.607925
Spike_AFFX-r2-Bs-phe_3-5-ratio1.261845
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5204,Count:9
Spike_AFFX-r2-P1-cre_5_signal3301.375732
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8766
Signal(M)15.351825
BackgroundAvg:88.25,Std:0.35,Min:87.5,Max:89.5
Spike_AFFX-r2-Ec-bioC_avg-signal259.935760
Spike_AFFX-r2-Bs-dap_avg-signal92.433289
Spike_AFFX-r2-Bs-dap_3-5-ratio3.001400
Spike_AFFX-r2-Ec-bioB_5_signal67.296097
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.507267
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-12_WT_120mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-12_WT_120mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-12_WT_120mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.820415
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.888073
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.008473
Spike_AFFX-r2-Bs-dap_5_signal39.124081
NoiseAvg:2.78,Std:0.06,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.904490
#P12637
Spike_AFFX-r2-Bs-phe_M_signal13.266308
Corner-Avg:6500,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.483749
Spike_AFFX-r2-Ec-bioB_3_signal83.655113
Spike_AFFX-r2-Bs-lys_M_signal8.165612
Spike_AFFX-r2-P1-cre_3_signal4243.825684
Spike_AFFX-r2-Bs-lys_3-5-ratio1.892338
Spike_AFFX-r2-Bs-dap_M_signal77.456535
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.153645
Spike_AFFX-r2-Ec-bioB_avg-signal88.697044
Spike_AFFX-r2-Bs-thr_avg-signal42.860775
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal856.842773
Spike_AFFX-r2-Bs-phe_5_signal23.420052
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1425.004272
RawQ2.627482
Spike_AFFX-r2-Bs-lys_5_signal11.044390
Signal(A)5.925468
%A42.722488
Signal(All)154.897232
Corner+Avg:80,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal355.611115
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.148085
Spike_AFFX-r2-Ec-bioD_avg-signal1140.923584
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P55.401138
Spike_AFFX-r2-Bs-lys_avg-signal13.369908
Spike_AFFX-r2-P1-cre_avg-signal4511.258789
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.876370
Spike_AFFX-r2-Bs-thr_3_signal59.618046
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.611481
Spike_AFFX-r2-Bs-dap_3_signal104.155098
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.663087
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal307.527649
#M428
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.899723
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.156355
Spike_AFFX-r2-Bs-thr_M_signal50.059780
Signal(P)274.298279
Spike_AFFX-r2-Bs-phe_3-5-ratio0.689498
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5433,Count:9
Spike_AFFX-r2-P1-cre_5_signal4778.691406
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9745
Signal(M)21.389696
BackgroundAvg:91.63,Std:0.34,Min:90.7,Max:93.4
Spike_AFFX-r2-Ec-bioC_avg-signal331.569397
Spike_AFFX-r2-Bs-dap_avg-signal73.578575
Spike_AFFX-r2-Bs-dap_3-5-ratio2.662174
Spike_AFFX-r2-Ec-bioB_5_signal82.952271
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.820415
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-13_WT_240mins_Rep2_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-13_WT_240mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-13_WT_240mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.761865
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.043179
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.085773
Spike_AFFX-r2-Bs-dap_5_signal34.818241
NoiseAvg:2.75,Std:0.20,Min:2.5,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.104702
#P13295
Spike_AFFX-r2-Bs-phe_M_signal19.681498
Corner-Avg:11207,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal114.381729
Spike_AFFX-r2-Ec-bioB_3_signal83.923874
Spike_AFFX-r2-Bs-lys_M_signal7.546098
Spike_AFFX-r2-P1-cre_3_signal4581.067383
Spike_AFFX-r2-Bs-lys_3-5-ratio1.731806
Spike_AFFX-r2-Bs-dap_M_signal73.173065
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.950657
Spike_AFFX-r2-Ec-bioB_avg-signal91.866577
Spike_AFFX-r2-Bs-thr_avg-signal30.104013
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal842.315796
Spike_AFFX-r2-Bs-phe_5_signal11.946766
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1311.539673
RawQ2.416994
Spike_AFFX-r2-Bs-lys_5_signal10.124461
Signal(A)4.969390
%A39.741341
Signal(All)153.172119
Corner+Avg:123,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal268.471283
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.828484
Spike_AFFX-r2-Ec-bioD_avg-signal1076.927734
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.285839
Spike_AFFX-r2-Bs-lys_avg-signal11.734721
Spike_AFFX-r2-P1-cre_avg-signal4486.258789
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.972819
Spike_AFFX-r2-Bs-thr_3_signal32.766167
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.152248
Spike_AFFX-r2-Bs-dap_3_signal143.936752
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.557064
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal267.278870
#M450
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.533604
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.004461
Spike_AFFX-r2-Bs-thr_M_signal46.441177
Signal(P)258.794250
Spike_AFFX-r2-Bs-phe_3-5-ratio2.413079
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9319,Count:9
Spike_AFFX-r2-P1-cre_5_signal4391.449707
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9065
Signal(M)18.085808
BackgroundAvg:61.65,Std:0.86,Min:60.1,Max:63.6
Spike_AFFX-r2-Ec-bioC_avg-signal267.875061
Spike_AFFX-r2-Bs-dap_avg-signal83.976021
Spike_AFFX-r2-Bs-dap_3-5-ratio4.133947
Spike_AFFX-r2-Ec-bioB_5_signal77.294128
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.761865
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-14_WT_480mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-14_WT_480mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-14_WT_480mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.601726
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.103824
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.367616
Spike_AFFX-r2-Bs-dap_5_signal49.779720
NoiseAvg:2.98,Std:0.14,Min:2.6,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.800606
#P13635
Spike_AFFX-r2-Bs-phe_M_signal21.534739
Corner-Avg:10413,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal79.938507
Spike_AFFX-r2-Ec-bioB_3_signal61.685688
Spike_AFFX-r2-Bs-lys_M_signal8.174503
Spike_AFFX-r2-P1-cre_3_signal3935.106934
Spike_AFFX-r2-Bs-lys_3-5-ratio1.130725
Spike_AFFX-r2-Bs-dap_M_signal81.904755
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.963929
Spike_AFFX-r2-Ec-bioB_avg-signal62.242908
Spike_AFFX-r2-Bs-thr_avg-signal36.090961
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal703.497986
Spike_AFFX-r2-Bs-phe_5_signal21.416067
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1179.473877
RawQ2.679648
Spike_AFFX-r2-Bs-lys_5_signal12.024823
Signal(A)3.844096
%A38.588337
Signal(All)150.604004
Corner+Avg:128,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.822479
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.286621
Spike_AFFX-r2-Ec-bioD_avg-signal941.485962
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.776413
Spike_AFFX-r2-Bs-lys_avg-signal11.265363
Spike_AFFX-r2-P1-cre_avg-signal3750.041504
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.635248
Spike_AFFX-r2-Bs-thr_3_signal40.850918
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.745810
Spike_AFFX-r2-Bs-dap_3_signal142.917831
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.676585
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal208.611023
#M373
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal13.596764
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.986633
Spike_AFFX-r2-Bs-thr_M_signal46.621365
Signal(P)249.042770
Spike_AFFX-r2-Bs-phe_3-5-ratio0.760486
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7843,Count:9
Spike_AFFX-r2-P1-cre_5_signal3564.976074
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8802
Signal(M)15.398093
BackgroundAvg:70.52,Std:1.12,Min:67.9,Max:73.3
Spike_AFFX-r2-Ec-bioC_avg-signal207.216751
Spike_AFFX-r2-Bs-dap_avg-signal91.534096
Spike_AFFX-r2-Bs-dap_3-5-ratio2.871005
Spike_AFFX-r2-Ec-bioB_5_signal45.104546
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.601726
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-15_WT_0mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-15_WT_0mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-15_WT_0mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.643555
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.063267
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.324064
Spike_AFFX-r2-Bs-dap_5_signal25.274950
NoiseAvg:2.68,Std:0.12,Min:2.3,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.713514
#P13496
Spike_AFFX-r2-Bs-phe_M_signal17.799839
Corner-Avg:10216,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal95.228287
Spike_AFFX-r2-Ec-bioB_3_signal76.508095
Spike_AFFX-r2-Bs-lys_M_signal14.448348
Spike_AFFX-r2-P1-cre_3_signal4497.128418
Spike_AFFX-r2-Bs-lys_3-5-ratio2.375752
Spike_AFFX-r2-Bs-dap_M_signal65.697006
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.706906
Spike_AFFX-r2-Ec-bioB_avg-signal76.506386
Spike_AFFX-r2-Bs-thr_avg-signal29.176895
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal977.222107
Spike_AFFX-r2-Bs-phe_5_signal22.520147
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1464.617920
RawQ2.562474
Spike_AFFX-r2-Bs-lys_5_signal11.564928
Signal(A)3.834787
%A39.127575
Signal(All)152.652069
Corner+Avg:117,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal262.763733
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.387007
Spike_AFFX-r2-Ec-bioD_avg-signal1220.920044
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.167030
Spike_AFFX-r2-Bs-lys_avg-signal17.829559
Spike_AFFX-r2-P1-cre_avg-signal4363.333496
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal43.420891
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.902330
Spike_AFFX-r2-Bs-dap_3_signal110.181992
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.498756
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal251.716232
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.475403
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.043889
Spike_AFFX-r2-Bs-thr_M_signal32.396282
Signal(P)255.021317
Spike_AFFX-r2-Bs-phe_3-5-ratio0.727660
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7793,Count:9
Spike_AFFX-r2-P1-cre_5_signal4229.538574
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8925
Signal(M)15.425477
BackgroundAvg:66.98,Std:0.44,Min:65.3,Max:67.8
Spike_AFFX-r2-Ec-bioC_avg-signal257.239990
Spike_AFFX-r2-Bs-dap_avg-signal67.051315
Spike_AFFX-r2-Bs-dap_3-5-ratio4.359336
Spike_AFFX-r2-Ec-bioB_5_signal57.782772
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.643555
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-16_WT_15mins_Rep3_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-16_WT_15mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-16_WT_15mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.804754
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.094383
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.807189
Spike_AFFX-r2-Bs-dap_5_signal47.955147
NoiseAvg:2.58,Std:0.07,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.611755
#P13030
Spike_AFFX-r2-Bs-phe_M_signal24.433969
Corner-Avg:10045,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.812210
Spike_AFFX-r2-Ec-bioB_3_signal53.811466
Spike_AFFX-r2-Bs-lys_M_signal9.702327
Spike_AFFX-r2-P1-cre_3_signal4490.915527
Spike_AFFX-r2-Bs-lys_3-5-ratio1.563017
Spike_AFFX-r2-Bs-dap_M_signal89.816032
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.142171
Spike_AFFX-r2-Ec-bioB_avg-signal70.762985
Spike_AFFX-r2-Bs-thr_avg-signal38.625179
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal809.839294
Spike_AFFX-r2-Bs-phe_5_signal14.392265
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1130.485962
RawQ2.355770
Spike_AFFX-r2-Bs-lys_5_signal15.877402
Signal(A)4.991269
%A41.074089
Signal(All)153.847122
Corner+Avg:121,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal231.290588
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.933672
Spike_AFFX-r2-Ec-bioD_avg-signal970.162598
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.124069
Spike_AFFX-r2-Bs-lys_avg-signal16.798792
Spike_AFFX-r2-P1-cre_avg-signal4297.260742
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.801841
Spike_AFFX-r2-Bs-thr_3_signal46.296085
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.919968
Spike_AFFX-r2-Bs-dap_3_signal150.904205
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.395939
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal221.742172
#M411
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.816648
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.043061
Spike_AFFX-r2-Bs-thr_M_signal47.967690
Signal(P)265.124451
Spike_AFFX-r2-Bs-phe_3-5-ratio1.871399
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6858,Count:9
Spike_AFFX-r2-P1-cre_5_signal4103.605957
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9369
Signal(M)19.265150
BackgroundAvg:83.99,Std:0.84,Min:81.2,Max:85.5
Spike_AFFX-r2-Ec-bioC_avg-signal226.516388
Spike_AFFX-r2-Bs-dap_avg-signal96.225128
Spike_AFFX-r2-Bs-dap_3-5-ratio3.146778
Spike_AFFX-r2-Ec-bioB_5_signal66.665283
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.804754
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-17_WT_30mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-17_WT_30mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-17_WT_30mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.688249
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.119330
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.782508
Spike_AFFX-r2-Bs-dap_5_signal31.260576
NoiseAvg:2.87,Std:0.10,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.897846
#P13460
Spike_AFFX-r2-Bs-phe_M_signal21.415081
Corner-Avg:11882,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.716003
Spike_AFFX-r2-Ec-bioB_3_signal76.689003
Spike_AFFX-r2-Bs-lys_M_signal7.720914
Spike_AFFX-r2-P1-cre_3_signal4229.080566
Spike_AFFX-r2-Bs-lys_3-5-ratio1.888326
Spike_AFFX-r2-Bs-dap_M_signal71.949440
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.682013
Spike_AFFX-r2-Ec-bioB_avg-signal72.142693
Spike_AFFX-r2-Bs-thr_avg-signal38.528122
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal851.147827
Spike_AFFX-r2-Bs-phe_5_signal17.796383
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1315.645630
RawQ2.623148
Spike_AFFX-r2-Bs-lys_5_signal12.218877
Signal(A)4.509996
%A39.333626
Signal(All)147.689240
Corner+Avg:125,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal233.404541
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.915051
Spike_AFFX-r2-Ec-bioD_avg-signal1083.396729
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.009205
Spike_AFFX-r2-Bs-lys_avg-signal14.337672
Spike_AFFX-r2-P1-cre_avg-signal4003.652344
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.657168
Spike_AFFX-r2-Bs-thr_3_signal58.536076
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.375504
Spike_AFFX-r2-Bs-dap_3_signal122.526077
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.545731
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal222.891190
#M378
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.073225
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.047168
Spike_AFFX-r2-Bs-thr_M_signal41.150440
Signal(P)246.782684
Spike_AFFX-r2-Bs-phe_3-5-ratio1.400006
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9774,Count:9
Spike_AFFX-r2-P1-cre_5_signal3778.224121
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8972
Signal(M)17.546999
BackgroundAvg:89.66,Std:0.49,Min:87.7,Max:90.6
Spike_AFFX-r2-Ec-bioC_avg-signal228.147858
Spike_AFFX-r2-Bs-dap_avg-signal75.245369
Spike_AFFX-r2-Bs-dap_3-5-ratio3.919508
Spike_AFFX-r2-Ec-bioB_5_signal43.023090
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.688249
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-18_WT_60mins_Rep3_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-18_WT_60mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-18_WT_60mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.579447
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.057548
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.412332
Spike_AFFX-r2-Bs-dap_5_signal10.960187
NoiseAvg:2.78,Std:0.07,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.307436
#P13769
Spike_AFFX-r2-Bs-phe_M_signal10.431720
Corner-Avg:11527,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.443550
Spike_AFFX-r2-Ec-bioB_3_signal80.169678
Spike_AFFX-r2-Bs-lys_M_signal7.492298
Spike_AFFX-r2-P1-cre_3_signal3932.832275
Spike_AFFX-r2-Bs-lys_3-5-ratio1.147653
Spike_AFFX-r2-Bs-dap_M_signal34.495522
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.846657
Spike_AFFX-r2-Ec-bioB_avg-signal75.459084
Spike_AFFX-r2-Bs-thr_avg-signal19.614958
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal814.652649
Spike_AFFX-r2-Bs-phe_5_signal10.192523
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1181.356323
RawQ2.485471
Spike_AFFX-r2-Bs-lys_5_signal7.111907
Signal(A)4.035691
%A37.948269
Signal(All)147.205643
Corner+Avg:126,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal243.332901
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.681386
Spike_AFFX-r2-Ec-bioD_avg-signal998.004517
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P60.363876
Spike_AFFX-r2-Bs-lys_avg-signal7.588735
Spike_AFFX-r2-P1-cre_avg-signal3825.826172
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.687856
Spike_AFFX-r2-Bs-thr_3_signal31.030760
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal11.435210
Spike_AFFX-r2-Bs-dap_3_signal62.860847
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.450135
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal223.395523
#M385
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal8.161999
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.089247
Spike_AFFX-r2-Bs-thr_M_signal22.506676
Signal(P)240.876190
Spike_AFFX-r2-Bs-phe_3-5-ratio1.342296
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10028,Count:9
Spike_AFFX-r2-P1-cre_5_signal3718.820068
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8656
Signal(M)16.112959
BackgroundAvg:86.31,Std:0.45,Min:84.7,Max:87.1
Spike_AFFX-r2-Ec-bioC_avg-signal233.364212
Spike_AFFX-r2-Bs-dap_avg-signal36.105518
Spike_AFFX-r2-Bs-dap_3-5-ratio5.735381
Spike_AFFX-r2-Ec-bioB_5_signal56.764042
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.579447
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-19_WT_120mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-19_WT_120mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-19_WT_120mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.511749
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.078692
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.331409
Spike_AFFX-r2-Bs-dap_5_signal59.861942
NoiseAvg:2.76,Std:0.10,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.096178
#P13872
Spike_AFFX-r2-Bs-phe_M_signal27.985027
Corner-Avg:12286,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal87.626747
Spike_AFFX-r2-Ec-bioB_3_signal78.532913
Spike_AFFX-r2-Bs-lys_M_signal25.403231
Spike_AFFX-r2-P1-cre_3_signal3747.852295
Spike_AFFX-r2-Bs-lys_3-5-ratio1.165041
Spike_AFFX-r2-Bs-dap_M_signal107.849243
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.919134
Spike_AFFX-r2-Ec-bioB_avg-signal75.048157
Spike_AFFX-r2-Bs-thr_avg-signal39.853119
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal756.575623
Spike_AFFX-r2-Bs-phe_5_signal28.108427
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1175.301880
RawQ2.412690
Spike_AFFX-r2-Bs-lys_5_signal18.729078
Signal(A)3.577035
%A37.750988
Signal(All)147.653488
Corner+Avg:147,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal217.396988
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.110281
Spike_AFFX-r2-Ec-bioD_avg-signal965.938721
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.815434
Spike_AFFX-r2-Bs-lys_avg-signal21.984148
Spike_AFFX-r2-P1-cre_avg-signal3611.146484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.433582
Spike_AFFX-r2-Bs-thr_3_signal52.825165
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.734579
Spike_AFFX-r2-Bs-dap_3_signal199.901154
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.553449
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal211.836990
#M327
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.820137
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.026247
Spike_AFFX-r2-Bs-thr_M_signal48.638012
Signal(P)240.250381
Spike_AFFX-r2-Bs-phe_3-5-ratio0.964489
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10307,Count:9
Spike_AFFX-r2-P1-cre_5_signal3474.440430
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8611
Signal(M)13.520056
BackgroundAvg:84.24,Std:0.55,Min:82.8,Max:85.5
Spike_AFFX-r2-Ec-bioC_avg-signal214.616989
Spike_AFFX-r2-Bs-dap_avg-signal122.537445
Spike_AFFX-r2-Bs-dap_3-5-ratio3.339370
Spike_AFFX-r2-Ec-bioB_5_signal58.984795
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.511749
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-20_WT_240mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-20_WT_240mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-20_WT_240mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.574281
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.159209
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.169206
Spike_AFFX-r2-Bs-dap_5_signal38.538235
NoiseAvg:3.08,Std:0.08,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.325434
#P13271
Spike_AFFX-r2-Bs-phe_M_signal18.838118
Corner-Avg:10642,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.981697
Spike_AFFX-r2-Ec-bioB_3_signal79.831741
Spike_AFFX-r2-Bs-lys_M_signal9.383787
Spike_AFFX-r2-P1-cre_3_signal4224.229004
Spike_AFFX-r2-Bs-lys_3-5-ratio3.070539
Spike_AFFX-r2-Bs-dap_M_signal61.066315
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.534728
Spike_AFFX-r2-Ec-bioB_avg-signal78.364014
Spike_AFFX-r2-Bs-thr_avg-signal26.953421
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal871.794189
Spike_AFFX-r2-Bs-phe_5_signal15.918157
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1269.184692
RawQ2.607274
Spike_AFFX-r2-Bs-lys_5_signal5.215733
Signal(A)4.398236
%A40.004383
Signal(All)149.389023
Corner+Avg:114,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal264.510254
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.764111
Spike_AFFX-r2-Ec-bioD_avg-signal1070.489502
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.180622
Spike_AFFX-r2-Bs-lys_avg-signal10.204877
Spike_AFFX-r2-P1-cre_avg-signal3934.145508
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.814993
Spike_AFFX-r2-Bs-thr_3_signal26.589836
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.840128
Spike_AFFX-r2-Bs-dap_3_signal96.195686
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.455831
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal223.726166
#M414
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.015112
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.182295
Spike_AFFX-r2-Bs-thr_M_signal36.944992
Signal(P)253.197891
Spike_AFFX-r2-Bs-phe_3-5-ratio1.367251
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9998,Count:9
Spike_AFFX-r2-P1-cre_5_signal3644.062012
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9125
Signal(M)17.488739
BackgroundAvg:93.16,Std:0.40,Min:91.9,Max:93.9
Spike_AFFX-r2-Ec-bioC_avg-signal244.118210
Spike_AFFX-r2-Bs-dap_avg-signal65.266747
Spike_AFFX-r2-Bs-dap_3-5-ratio2.496110
Spike_AFFX-r2-Ec-bioB_5_signal68.278595
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.574281
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-21_WT_480mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-21_WT_480mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-21_WT_480mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.802335
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.136480
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.986689
Spike_AFFX-r2-Bs-dap_5_signal45.575008
NoiseAvg:2.68,Std:0.17,Min:2.3,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.475292
#P13156
Spike_AFFX-r2-Bs-phe_M_signal21.291494
Corner-Avg:10046,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.293587
Spike_AFFX-r2-Ec-bioB_3_signal76.907173
Spike_AFFX-r2-Bs-lys_M_signal13.000420
Spike_AFFX-r2-P1-cre_3_signal4957.605957
Spike_AFFX-r2-Bs-lys_3-5-ratio1.688113
Spike_AFFX-r2-Bs-dap_M_signal85.990341
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.779086
Spike_AFFX-r2-Ec-bioB_avg-signal85.715149
Spike_AFFX-r2-Bs-thr_avg-signal39.214237
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1008.990540
Spike_AFFX-r2-Bs-phe_5_signal22.419956
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1464.174805
RawQ2.552029
Spike_AFFX-r2-Bs-lys_5_signal13.561126
Signal(A)4.959590
%A40.640072
Signal(All)154.352646
Corner+Avg:118,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal251.547104
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.074196
Spike_AFFX-r2-Ec-bioD_avg-signal1236.582642
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.676456
Spike_AFFX-r2-Bs-lys_avg-signal16.484751
Spike_AFFX-r2-P1-cre_avg-signal4659.926758
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.683472
Spike_AFFX-r2-Bs-thr_3_signal51.344421
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.595215
Spike_AFFX-r2-Bs-dap_3_signal142.406540
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.451128
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal256.588898
#M384
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.892708
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.980351
Spike_AFFX-r2-Bs-thr_M_signal47.823002
Signal(P)263.592316
Spike_AFFX-r2-Bs-phe_3-5-ratio1.475212
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7108,Count:9
Spike_AFFX-r2-P1-cre_5_signal4362.247070
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9270
Signal(M)18.197948
BackgroundAvg:86.28,Std:0.45,Min:85.0,Max:87.5
Spike_AFFX-r2-Ec-bioC_avg-signal254.067993
Spike_AFFX-r2-Bs-dap_avg-signal91.323967
Spike_AFFX-r2-Bs-dap_3-5-ratio3.124663
Spike_AFFX-r2-Ec-bioB_5_signal77.944702
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.802335
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-22_WT_0mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-22_WT_0mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-22_WT_0mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.900441
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.981330
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.662822
Spike_AFFX-r2-Bs-dap_5_signal35.387875
NoiseAvg:3.15,Std:0.17,Min:2.6,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.546356
#P12493
Spike_AFFX-r2-Bs-phe_M_signal25.787266
Corner-Avg:10093,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.375931
Spike_AFFX-r2-Ec-bioB_3_signal44.027485
Spike_AFFX-r2-Bs-lys_M_signal10.559192
Spike_AFFX-r2-P1-cre_3_signal4103.083008
Spike_AFFX-r2-Bs-lys_3-5-ratio0.812244
Spike_AFFX-r2-Bs-dap_M_signal48.515213
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.683008
Spike_AFFX-r2-Ec-bioB_avg-signal63.942585
Spike_AFFX-r2-Bs-thr_avg-signal36.575695
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal695.457214
Spike_AFFX-r2-Bs-phe_5_signal17.019089
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1216.885986
RawQ2.697624
Spike_AFFX-r2-Bs-lys_5_signal9.164584
Signal(A)6.360518
%A43.125820
Signal(All)151.394073
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal203.290527
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal12.585210
Spike_AFFX-r2-Ec-bioD_avg-signal956.171631
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P54.769836
Spike_AFFX-r2-Bs-lys_avg-signal9.055885
Spike_AFFX-r2-P1-cre_avg-signal4142.113281
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.104340
Spike_AFFX-r2-Bs-thr_3_signal49.760029
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.463854
Spike_AFFX-r2-Bs-dap_3_signal67.170998
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.749764
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal177.419449
#M480
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal7.443879
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.145819
Spike_AFFX-r2-Bs-thr_M_signal41.420696
Signal(P)270.535065
Spike_AFFX-r2-Bs-phe_3-5-ratio0.739476
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9044,Count:9
Spike_AFFX-r2-P1-cre_5_signal4181.143555
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9837
Signal(M)22.782635
BackgroundAvg:98.36,Std:1.47,Min:95.0,Max:101.9
Spike_AFFX-r2-Ec-bioC_avg-signal190.354980
Spike_AFFX-r2-Bs-dap_avg-signal50.358028
Spike_AFFX-r2-Bs-dap_3-5-ratio1.898136
Spike_AFFX-r2-Ec-bioB_5_signal66.424339
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.900441
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-23_WT_15mins_Rep4_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-23_WT_15mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-23_WT_15mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.64507
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.152245
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.291323
Spike_AFFX-r2-Bs-dap_5_signal58.199184
NoiseAvg:2.60,Std:0.10,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.455091
#P13532
Spike_AFFX-r2-Bs-phe_M_signal32.492508
Corner-Avg:10533,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.658463
Spike_AFFX-r2-Ec-bioB_3_signal74.291748
Spike_AFFX-r2-Bs-lys_M_signal15.428517
Spike_AFFX-r2-P1-cre_3_signal4354.465332
Spike_AFFX-r2-Bs-lys_3-5-ratio2.114188
Spike_AFFX-r2-Bs-dap_M_signal120.512924
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.204934
Spike_AFFX-r2-Ec-bioB_avg-signal73.493904
Spike_AFFX-r2-Bs-thr_avg-signal46.511044
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal792.691284
Spike_AFFX-r2-Bs-phe_5_signal28.730452
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1139.338989
RawQ2.473505
Spike_AFFX-r2-Bs-lys_5_signal14.383350
Signal(A)3.697592
%A39.153881
Signal(All)148.688400
Corner+Avg:108,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal217.227310
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal38.941517
Spike_AFFX-r2-Ec-bioD_avg-signal966.015137
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.324856
Spike_AFFX-r2-Bs-lys_avg-signal20.073656
Spike_AFFX-r2-P1-cre_avg-signal4066.789307
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.521263
Spike_AFFX-r2-Bs-thr_3_signal69.192566
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal33.388157
Spike_AFFX-r2-Bs-dap_3_signal189.398376
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.437305
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal212.064087
#M347
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.409101
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.024347
Spike_AFFX-r2-Bs-thr_M_signal53.885471
Signal(P)247.799362
Spike_AFFX-r2-Bs-phe_3-5-ratio1.355409
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9819,Count:9
Spike_AFFX-r2-P1-cre_5_signal3779.113281
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8931
Signal(M)15.383643
BackgroundAvg:87.34,Std:0.85,Min:85.0,Max:89.2
Spike_AFFX-r2-Ec-bioC_avg-signal214.645691
Spike_AFFX-r2-Bs-dap_avg-signal122.703499
Spike_AFFX-r2-Bs-dap_3-5-ratio3.254313
Spike_AFFX-r2-Ec-bioB_5_signal57.531502
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.645070
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-24_WT_30mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-24_WT_30mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-24_WT_30mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.897476
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.091871
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.136572
Spike_AFFX-r2-Bs-dap_5_signal121.430954
NoiseAvg:2.44,Std:0.11,Min:2.2,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal46.747906
#P13029
Spike_AFFX-r2-Bs-phe_M_signal50.999767
Corner-Avg:11756,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal109.208870
Spike_AFFX-r2-Ec-bioB_3_signal79.434952
Spike_AFFX-r2-Bs-lys_M_signal32.634148
Spike_AFFX-r2-P1-cre_3_signal4271.061035
Spike_AFFX-r2-Bs-lys_3-5-ratio1.769301
Spike_AFFX-r2-Bs-dap_M_signal218.513199
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.328374
Spike_AFFX-r2-Ec-bioB_avg-signal86.177917
Spike_AFFX-r2-Bs-thr_avg-signal103.347687
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal794.334961
Spike_AFFX-r2-Bs-phe_5_signal43.259651
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1427.690063
RawQ2.363879
Spike_AFFX-r2-Bs-lys_5_signal30.376858
Signal(A)5.065055
%A41.052170
Signal(All)149.658905
Corner+Avg:119,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal238.014526
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal69.014557
Spike_AFFX-r2-Ec-bioD_avg-signal1111.012451
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.119686
Spike_AFFX-r2-Bs-lys_avg-signal38.918941
Spike_AFFX-r2-P1-cre_avg-signal4091.375488
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.828146
Spike_AFFX-r2-Bs-thr_3_signal155.594513
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal54.424664
Spike_AFFX-r2-Bs-dap_3_signal298.327362
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.797340
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal240.057922
#M417
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.745811
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.991488
Spike_AFFX-r2-Bs-thr_M_signal107.700661
Signal(P)257.788635
Spike_AFFX-r2-Bs-phe_3-5-ratio1.595356
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9078,Count:9
Spike_AFFX-r2-P1-cre_5_signal3911.689697
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9364
Signal(M)18.135006
BackgroundAvg:83.27,Std:1.03,Min:80.4,Max:85.5
Spike_AFFX-r2-Ec-bioC_avg-signal239.036224
Spike_AFFX-r2-Bs-dap_avg-signal212.757187
Spike_AFFX-r2-Bs-dap_3-5-ratio2.456765
Spike_AFFX-r2-Ec-bioB_5_signal69.889938
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.897476
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-25_WT_60mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-25_WT_60mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-25_WT_60mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.490584
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.080222
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.890888
Spike_AFFX-r2-Bs-dap_5_signal45.634621
NoiseAvg:3.02,Std:0.30,Min:2.6,Max:5.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.845818
#P13849
Spike_AFFX-r2-Bs-phe_M_signal19.673582
Corner-Avg:7578,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.939491
Spike_AFFX-r2-Ec-bioB_3_signal67.845688
Spike_AFFX-r2-Bs-lys_M_signal12.369412
Spike_AFFX-r2-P1-cre_3_signal3574.839600
Spike_AFFX-r2-Bs-lys_3-5-ratio2.129745
Spike_AFFX-r2-Bs-dap_M_signal91.752632
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.599965
Spike_AFFX-r2-Ec-bioB_avg-signal78.313438
Spike_AFFX-r2-Bs-thr_avg-signal38.650799
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal685.103394
Spike_AFFX-r2-Bs-phe_5_signal23.219290
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1014.271729
RawQ2.393910
Spike_AFFX-r2-Bs-lys_5_signal10.582785
Signal(A)3.981474
%A37.693993
Signal(All)143.567627
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal267.549164
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.392675
Spike_AFFX-r2-Ec-bioD_avg-signal849.687561
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.714600
Spike_AFFX-r2-Bs-lys_avg-signal15.163612
Spike_AFFX-r2-P1-cre_avg-signal3442.097656
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal57.044388
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.428514
Spike_AFFX-r2-Bs-dap_3_signal132.914551
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.480465
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal247.049545
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.538639
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.082978
Spike_AFFX-r2-Bs-thr_M_signal43.062195
Signal(P)233.597000
Spike_AFFX-r2-Bs-phe_3-5-ratio0.921332
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6084,Count:9
Spike_AFFX-r2-P1-cre_5_signal3309.355713
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8598
Signal(M)15.041924
BackgroundAvg:85.03,Std:0.51,Min:83.5,Max:86.5
Spike_AFFX-r2-Ec-bioC_avg-signal257.299347
Spike_AFFX-r2-Bs-dap_avg-signal90.100594
Spike_AFFX-r2-Bs-dap_3-5-ratio2.912581
Spike_AFFX-r2-Ec-bioB_5_signal76.155128
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.490584
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-26_WT_120mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-26_WT_120mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-26_WT_120mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.531461
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.081476
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.231856
Spike_AFFX-r2-Bs-dap_5_signal43.567440
NoiseAvg:3.46,Std:0.10,Min:3.2,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.539782
#P13321
Spike_AFFX-r2-Bs-phe_M_signal16.441685
Corner-Avg:11319,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal72.265312
Spike_AFFX-r2-Ec-bioB_3_signal61.098133
Spike_AFFX-r2-Bs-lys_M_signal6.906177
Spike_AFFX-r2-P1-cre_3_signal3189.547119
Spike_AFFX-r2-Bs-lys_3-5-ratio2.221789
Spike_AFFX-r2-Bs-dap_M_signal94.617897
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.994166
Spike_AFFX-r2-Ec-bioB_avg-signal60.987293
Spike_AFFX-r2-Bs-thr_avg-signal37.111416
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal601.123413
Spike_AFFX-r2-Bs-phe_5_signal21.526714
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal926.053284
RawQ2.901851
Spike_AFFX-r2-Bs-lys_5_signal11.996838
Signal(A)4.425398
%A39.820255
Signal(All)145.007065
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.592773
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.118113
Spike_AFFX-r2-Ec-bioD_avg-signal763.588379
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.399826
Spike_AFFX-r2-Bs-lys_avg-signal15.185818
Spike_AFFX-r2-P1-cre_avg-signal3069.400391
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.779921
Spike_AFFX-r2-Bs-thr_3_signal58.074303
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.362173
Spike_AFFX-r2-Bs-dap_3_signal120.561363
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.540538
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal180.790878
#M406
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.654438
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.137186
Spike_AFFX-r2-Bs-thr_M_signal38.720158
Signal(P)244.759644
Spike_AFFX-r2-Bs-phe_3-5-ratio1.213288
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8724,Count:9
Spike_AFFX-r2-P1-cre_5_signal2949.253418
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9083
Signal(M)17.172457
BackgroundAvg:100.99,Std:0.70,Min:99.2,Max:103.1
Spike_AFFX-r2-Ec-bioC_avg-signal193.191833
Spike_AFFX-r2-Bs-dap_avg-signal86.248901
Spike_AFFX-r2-Bs-dap_3-5-ratio2.767236
Spike_AFFX-r2-Ec-bioB_5_signal49.598434
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.531461
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-27_WT_240mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-27_WT_240mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-27_WT_240mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.721509
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.022097
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.689368
Spike_AFFX-r2-Bs-dap_5_signal62.932869
NoiseAvg:3.22,Std:0.06,Min:3.0,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.984352
#P13029
Spike_AFFX-r2-Bs-phe_M_signal21.570950
Corner-Avg:10645,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal94.628769
Spike_AFFX-r2-Ec-bioB_3_signal76.372231
Spike_AFFX-r2-Bs-lys_M_signal9.569997
Spike_AFFX-r2-P1-cre_3_signal3390.345703
Spike_AFFX-r2-Bs-lys_3-5-ratio1.517275
Spike_AFFX-r2-Bs-dap_M_signal85.227188
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.535067
Spike_AFFX-r2-Ec-bioB_avg-signal72.069527
Spike_AFFX-r2-Bs-thr_avg-signal37.658047
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal699.097717
Spike_AFFX-r2-Bs-phe_5_signal14.019026
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1130.809937
RawQ2.846112
Spike_AFFX-r2-Bs-lys_5_signal12.111849
Signal(A)5.065569
%A41.104778
Signal(All)147.799469
Corner+Avg:125,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal245.533875
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.011166
Spike_AFFX-r2-Ec-bioD_avg-signal914.953857
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.119686
Spike_AFFX-r2-Bs-lys_avg-signal13.352951
Spike_AFFX-r2-P1-cre_avg-signal3353.698242
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.775537
Spike_AFFX-r2-Bs-thr_3_signal48.126606
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.200380
Spike_AFFX-r2-Bs-dap_3_signal131.907043
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.617528
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal205.844666
#M405
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.377007
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.192811
Spike_AFFX-r2-Bs-thr_M_signal45.863186
Signal(P)254.526138
Spike_AFFX-r2-Bs-phe_3-5-ratio1.142103
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9189,Count:9
Spike_AFFX-r2-P1-cre_5_signal3317.050537
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9376
Signal(M)18.741049
BackgroundAvg:101.67,Std:0.41,Min:100.1,Max:102.5
Spike_AFFX-r2-Ec-bioC_avg-signal225.689270
Spike_AFFX-r2-Bs-dap_avg-signal93.355705
Spike_AFFX-r2-Bs-dap_3-5-ratio2.095996
Spike_AFFX-r2-Ec-bioB_5_signal45.207561
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.721509
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-28_WT_480mins_Rep4_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-28_WT_480mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-28_WT_480mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.615117
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.990422
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.027847
Spike_AFFX-r2-Bs-dap_5_signal41.031349
NoiseAvg:2.88,Std:0.07,Min:2.7,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.423328
#P13221
Spike_AFFX-r2-Bs-phe_M_signal17.081419
Corner-Avg:6815,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.221191
Spike_AFFX-r2-Ec-bioB_3_signal67.800148
Spike_AFFX-r2-Bs-lys_M_signal8.429428
Spike_AFFX-r2-P1-cre_3_signal3455.119141
Spike_AFFX-r2-Bs-lys_3-5-ratio2.348371
Spike_AFFX-r2-Bs-dap_M_signal67.121010
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.010031
Spike_AFFX-r2-Ec-bioB_avg-signal74.661522
Spike_AFFX-r2-Bs-thr_avg-signal35.825428
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal597.817200
Spike_AFFX-r2-Bs-phe_5_signal18.888809
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal933.135193
RawQ2.678829
Spike_AFFX-r2-Bs-lys_5_signal8.727725
Signal(A)4.670932
%A40.311268
Signal(All)147.090591
Corner+Avg:91,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal283.438110
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.690372
Spike_AFFX-r2-Ec-bioD_avg-signal765.476196
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P57.961422
Spike_AFFX-r2-Bs-lys_avg-signal12.551030
Spike_AFFX-r2-P1-cre_avg-signal3471.825439
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.727313
Spike_AFFX-r2-Bs-thr_3_signal53.827965
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.220200
Spike_AFFX-r2-Bs-dap_3_signal96.201988
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.560904
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal236.621857
#M394
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.495939
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.197853
Spike_AFFX-r2-Bs-thr_M_signal40.224991
Signal(P)249.990326
Spike_AFFX-r2-Bs-phe_3-5-ratio0.989495
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5384,Count:9
Spike_AFFX-r2-P1-cre_5_signal3488.531738
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9195
Signal(M)17.931894
BackgroundAvg:93.78,Std:0.55,Min:91.8,Max:95.2
Spike_AFFX-r2-Ec-bioC_avg-signal260.029968
Spike_AFFX-r2-Bs-dap_avg-signal68.118111
Spike_AFFX-r2-Bs-dap_3-5-ratio2.344597
Spike_AFFX-r2-Ec-bioB_5_signal65.963242
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.615117
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-29_arf7/19_0mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-29_arf7/19_0mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-29_arf7/19_0mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.676678
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.115659
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.735347
Spike_AFFX-r2-Bs-dap_5_signal43.850227
NoiseAvg:3.17,Std:0.12,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.681873
#P13235
Spike_AFFX-r2-Bs-phe_M_signal10.661736
Corner-Avg:12163,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal100.015114
Spike_AFFX-r2-Ec-bioB_3_signal97.501472
Spike_AFFX-r2-Bs-lys_M_signal10.611327
Spike_AFFX-r2-P1-cre_3_signal3965.849365
Spike_AFFX-r2-Bs-lys_3-5-ratio1.430993
Spike_AFFX-r2-Bs-dap_M_signal94.013008
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.579496
Spike_AFFX-r2-Ec-bioB_avg-signal84.567390
Spike_AFFX-r2-Bs-thr_avg-signal33.417404
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal778.171387
Spike_AFFX-r2-Bs-phe_5_signal21.845762
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1226.366943
RawQ2.789660
Spike_AFFX-r2-Bs-lys_5_signal15.894696
Signal(A)4.838934
%A40.214817
Signal(All)148.938538
Corner+Avg:139,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal275.680573
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.500175
Spike_AFFX-r2-Ec-bioD_avg-signal1002.269165
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.022797
Spike_AFFX-r2-Bs-lys_avg-signal16.417072
Spike_AFFX-r2-P1-cre_avg-signal3760.282227
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.762385
Spike_AFFX-r2-Bs-thr_3_signal37.405426
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.335892
Spike_AFFX-r2-Bs-dap_3_signal173.353683
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.575960
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal224.490845
#M402
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.745195
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.228026
Spike_AFFX-r2-Bs-thr_M_signal39.164913
Signal(P)252.790833
Spike_AFFX-r2-Bs-phe_3-5-ratio1.304609
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10640,Count:9
Spike_AFFX-r2-P1-cre_5_signal3554.715088
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9173
Signal(M)17.944698
BackgroundAvg:98.59,Std:0.59,Min:96.6,Max:100.2
Spike_AFFX-r2-Ec-bioC_avg-signal250.085709
Spike_AFFX-r2-Bs-dap_avg-signal103.738976
Spike_AFFX-r2-Bs-dap_3-5-ratio3.953313
Spike_AFFX-r2-Ec-bioB_5_signal56.185593
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.676678
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-30_arf7/19_15mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-30_arf7/19_15mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-30_arf7/19_15mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.708514
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.089655
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.371393
Spike_AFFX-r2-Bs-dap_5_signal67.805130
NoiseAvg:2.73,Std:0.07,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.082703
#P13227
Spike_AFFX-r2-Bs-phe_M_signal22.680161
Corner-Avg:12717,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.294449
Spike_AFFX-r2-Ec-bioB_3_signal79.191483
Spike_AFFX-r2-Bs-lys_M_signal9.523200
Spike_AFFX-r2-P1-cre_3_signal4277.747070
Spike_AFFX-r2-Bs-lys_3-5-ratio1.920130
Spike_AFFX-r2-Bs-dap_M_signal126.048088
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.414970
Spike_AFFX-r2-Ec-bioB_avg-signal77.743744
Spike_AFFX-r2-Bs-thr_avg-signal39.139801
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal915.788208
Spike_AFFX-r2-Bs-phe_5_signal35.663784
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1226.160889
RawQ2.493308
Spike_AFFX-r2-Bs-lys_5_signal17.707672
Signal(A)4.777169
%A40.074528
Signal(All)148.916580
Corner+Avg:153,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal280.015198
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.879677
Spike_AFFX-r2-Ec-bioD_avg-signal1070.974609
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.987724
Spike_AFFX-r2-Bs-lys_avg-signal20.410633
Spike_AFFX-r2-P1-cre_avg-signal4101.763672
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.937747
Spike_AFFX-r2-Bs-thr_3_signal50.914101
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.074539
Spike_AFFX-r2-Bs-dap_3_signal179.228027
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.338913
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal210.544785
#M442
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.001026
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.329955
Spike_AFFX-r2-Bs-thr_M_signal45.422600
Signal(P)252.905518
Spike_AFFX-r2-Bs-phe_3-5-ratio0.978014
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10023,Count:9
Spike_AFFX-r2-P1-cre_5_signal3925.780029
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9141
Signal(M)17.959253
BackgroundAvg:88.02,Std:0.49,Min:87.0,Max:89.5
Spike_AFFX-r2-Ec-bioC_avg-signal245.279999
Spike_AFFX-r2-Bs-dap_avg-signal124.360413
Spike_AFFX-r2-Bs-dap_3-5-ratio2.643281
Spike_AFFX-r2-Ec-bioB_5_signal57.745304
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.708514
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-31_arf7/19_30mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-31_arf7/19_30mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-31_arf7/19_30mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.75344
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.026492
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.459683
Spike_AFFX-r2-Bs-dap_5_signal51.004749
NoiseAvg:3.36,Std:0.11,Min:3.0,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.958614
#P13089
Spike_AFFX-r2-Bs-phe_M_signal28.921675
Corner-Avg:13113,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal117.983948
Spike_AFFX-r2-Ec-bioB_3_signal92.917938
Spike_AFFX-r2-Bs-lys_M_signal14.226597
Spike_AFFX-r2-P1-cre_3_signal3707.525146
Spike_AFFX-r2-Bs-lys_3-5-ratio1.129861
Spike_AFFX-r2-Bs-dap_M_signal90.547844
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.534301
Spike_AFFX-r2-Ec-bioB_avg-signal91.519379
Spike_AFFX-r2-Bs-thr_avg-signal35.698376
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal759.690857
Spike_AFFX-r2-Bs-phe_5_signal18.865488
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1326.365723
RawQ2.929461
Spike_AFFX-r2-Bs-lys_5_signal15.506535
Signal(A)5.279051
%A40.894344
Signal(All)151.680008
Corner+Avg:151,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal259.355804
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.698442
Spike_AFFX-r2-Ec-bioD_avg-signal1043.028320
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.382729
Spike_AFFX-r2-Bs-lys_avg-signal15.751122
Spike_AFFX-r2-P1-cre_avg-signal3659.683594
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal50.581142
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal24.828535
Spike_AFFX-r2-Bs-dap_3_signal118.846313
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.745928
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.006973
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.520231
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.085139
Spike_AFFX-r2-Bs-thr_M_signal36.555367
Signal(P)259.986755
Spike_AFFX-r2-Bs-phe_3-5-ratio1.415200
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11176,Count:9
Spike_AFFX-r2-P1-cre_5_signal3611.842041
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9328
Signal(M)19.366669
BackgroundAvg:81.17,Std:1.17,Min:78.1,Max:83.9
Spike_AFFX-r2-Ec-bioC_avg-signal249.181396
Spike_AFFX-r2-Bs-dap_avg-signal86.799644
Spike_AFFX-r2-Bs-dap_3-5-ratio2.330103
Spike_AFFX-r2-Ec-bioB_5_signal63.656254
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.753440
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-32_arf7/19_60mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-32_arf7/19_60mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-32_arf7/19_60mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.565435
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.139051
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.402731
Spike_AFFX-r2-Bs-dap_5_signal55.256393
NoiseAvg:2.99,Std:0.10,Min:2.8,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.598997
#P13409
Spike_AFFX-r2-Bs-phe_M_signal19.800402
Corner-Avg:13481,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal114.642563
Spike_AFFX-r2-Ec-bioB_3_signal96.004936
Spike_AFFX-r2-Bs-lys_M_signal14.600974
Spike_AFFX-r2-P1-cre_3_signal4122.198242
Spike_AFFX-r2-Bs-lys_3-5-ratio1.515311
Spike_AFFX-r2-Bs-dap_M_signal113.042618
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.866417
Spike_AFFX-r2-Ec-bioB_avg-signal93.029655
Spike_AFFX-r2-Bs-thr_avg-signal45.382370
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal951.625244
Spike_AFFX-r2-Bs-phe_5_signal21.544037
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1417.279175
RawQ2.433558
Spike_AFFX-r2-Bs-lys_5_signal11.193568
Signal(A)5.100725
%A39.329243
Signal(All)146.940475
Corner+Avg:158,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal283.478516
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.932371
Spike_AFFX-r2-Ec-bioD_avg-signal1184.452148
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.785622
Spike_AFFX-r2-Bs-lys_avg-signal14.252091
Spike_AFFX-r2-P1-cre_avg-signal3870.587402
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal71.911484
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.425604
Spike_AFFX-r2-Bs-dap_3_signal168.586304
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.489325
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.700775
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.961733
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.153755
Spike_AFFX-r2-Bs-thr_M_signal45.636635
Signal(P)245.967316
Spike_AFFX-r2-Bs-phe_3-5-ratio1.342941
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11221,Count:9
Spike_AFFX-r2-P1-cre_5_signal3618.976807
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8971
Signal(M)18.088017
BackgroundAvg:87.56,Std:0.67,Min:85.7,Max:89.6
Spike_AFFX-r2-Ec-bioC_avg-signal264.589661
Spike_AFFX-r2-Bs-dap_avg-signal112.295105
Spike_AFFX-r2-Bs-dap_3-5-ratio3.050983
Spike_AFFX-r2-Ec-bioB_5_signal68.441467
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.565435
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-33_arf7/19_120mins_Rep1_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-33_arf7/19_120mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-33_arf7/19_120mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:1.033898
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.046092
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.108442
Spike_AFFX-r2-Bs-dap_5_signal40.253246
NoiseAvg:3.86,Std:0.16,Min:3.6,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.473215
#P12057
Spike_AFFX-r2-Bs-phe_M_signal7.764109
Corner-Avg:10987,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal168.248047
Spike_AFFX-r2-Ec-bioB_3_signal123.154457
Spike_AFFX-r2-Bs-lys_M_signal12.317140
Spike_AFFX-r2-P1-cre_3_signal5879.286133
Spike_AFFX-r2-Bs-lys_3-5-ratio2.403773
Spike_AFFX-r2-Bs-dap_M_signal58.219692
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.426312
Spike_AFFX-r2-Ec-bioB_avg-signal134.169479
Spike_AFFX-r2-Bs-thr_avg-signal28.540962
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1410.187134
Spike_AFFX-r2-Bs-phe_5_signal16.016773
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2056.262695
RawQ3.328326
Spike_AFFX-r2-Bs-lys_5_signal8.271624
Signal(A)7.856526
%A45.107410
Signal(All)157.284286
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal295.877594
Spike_AFFX-r2-Bs-lys_3_detectionM
Spike_AFFX-r2-Bs-phe_3_signal11.807951
Spike_AFFX-r2-Ec-bioD_avg-signal1733.224854
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P52.858395
Spike_AFFX-r2-Bs-lys_avg-signal13.490621
Spike_AFFX-r2-P1-cre_avg-signal5749.763672
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.034195
Spike_AFFX-r2-Bs-thr_3_signal39.969166
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal11.862945
Spike_AFFX-r2-Bs-dap_3_signal106.460808
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.458149
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal382.682159
#M464
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal19.883102
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.773168
Spike_AFFX-r2-Bs-thr_M_signal29.180506
Signal(P)289.855286
Spike_AFFX-r2-Bs-phe_3-5-ratio0.737224
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8272,Count:9
Spike_AFFX-r2-P1-cre_5_signal5620.240723
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10289
Signal(M)25.934574
BackgroundAvg:101.85,Std:1.06,Min:98.3,Max:104.1
Spike_AFFX-r2-Ec-bioC_avg-signal339.279877
Spike_AFFX-r2-Bs-dap_avg-signal68.311249
Spike_AFFX-r2-Bs-dap_3-5-ratio2.644776
Spike_AFFX-r2-Ec-bioB_5_signal111.105942
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.033898
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-34_arf7/19_240mins_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-34_arf7/19_240mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-34_arf7/19_240mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.848975
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.047442
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.255101
Spike_AFFX-r2-Bs-dap_5_signal50.817528
NoiseAvg:2.78,Std:0.08,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.943045
#P13142
Spike_AFFX-r2-Bs-phe_M_signal22.415159
Corner-Avg:9569,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal132.848907
Spike_AFFX-r2-Ec-bioB_3_signal84.947983
Spike_AFFX-r2-Bs-lys_M_signal14.516525
Spike_AFFX-r2-P1-cre_3_signal4730.415527
Spike_AFFX-r2-Bs-lys_3-5-ratio1.609830
Spike_AFFX-r2-Bs-dap_M_signal111.512276
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.839805
Spike_AFFX-r2-Ec-bioB_avg-signal95.159698
Spike_AFFX-r2-Bs-thr_avg-signal39.203674
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1058.866821
Spike_AFFX-r2-Bs-phe_5_signal22.001307
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1660.078369
RawQ2.556947
Spike_AFFX-r2-Bs-lys_5_signal8.765250
Signal(A)5.093794
%A40.499783
Signal(All)151.128952
Corner+Avg:112,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal277.410919
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal35.279690
Spike_AFFX-r2-Ec-bioD_avg-signal1359.472656
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.615082
Spike_AFFX-r2-Bs-lys_avg-signal12.464112
Spike_AFFX-r2-P1-cre_avg-signal4623.288574
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal53.794548
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.565384
Spike_AFFX-r2-Bs-dap_3_signal109.349998
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.567788
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal290.789246
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.110562
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.953993
Spike_AFFX-r2-Bs-thr_M_signal44.873428
Signal(P)258.140961
Spike_AFFX-r2-Bs-phe_3-5-ratio1.603527
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8275,Count:9
Spike_AFFX-r2-P1-cre_5_signal4516.161621
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9238
Signal(M)17.922132
BackgroundAvg:70.63,Std:0.71,Min:68.7,Max:72.5
Spike_AFFX-r2-Ec-bioC_avg-signal284.100098
Spike_AFFX-r2-Bs-dap_avg-signal90.559937
Spike_AFFX-r2-Bs-dap_3-5-ratio2.151817
Spike_AFFX-r2-Ec-bioB_5_signal67.682198
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.848975
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-35_arf7/19_480mins_Rep1_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-35_arf7/19_480mins_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-35_arf7/19_480mins_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4°C, dark.
Sterilisation. Sterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: Primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.742056
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.146063
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.931736
Spike_AFFX-r2-Bs-dap_5_signal71.277397
NoiseAvg:2.61,Std:0.06,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.448328
#P13650
Spike_AFFX-r2-Bs-phe_M_signal22.644724
Corner-Avg:11756,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.872871
Spike_AFFX-r2-Ec-bioB_3_signal80.247429
Spike_AFFX-r2-Bs-lys_M_signal9.022286
Spike_AFFX-r2-P1-cre_3_signal4505.625977
Spike_AFFX-r2-Bs-lys_3-5-ratio2.366066
Spike_AFFX-r2-Bs-dap_M_signal125.118248
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.719871
Spike_AFFX-r2-Ec-bioB_avg-signal95.415703
Spike_AFFX-r2-Bs-thr_avg-signal37.612335
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal813.901001
Spike_AFFX-r2-Bs-phe_5_signal27.924402
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1196.960938
RawQ2.407102
Spike_AFFX-r2-Bs-lys_5_signal12.464029
Signal(A)4.356568
%A38.526962
Signal(All)148.233795
Corner+Avg:130,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal284.744110
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.413403
Spike_AFFX-r2-Ec-bioD_avg-signal1005.430969
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.842175
Spike_AFFX-r2-Bs-lys_avg-signal16.992342
Spike_AFFX-r2-P1-cre_avg-signal4218.509766
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.630864
Spike_AFFX-r2-Bs-thr_3_signal42.047962
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal28.327509
Spike_AFFX-r2-Bs-dap_3_signal150.722534
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.470647
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal256.369476
#M372
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.490715
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.110679
Spike_AFFX-r2-Bs-thr_M_signal46.340717
Signal(P)244.469559
Spike_AFFX-r2-Bs-phe_3-5-ratio1.232377
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9398,Count:9
Spike_AFFX-r2-P1-cre_5_signal3931.393555
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8788
Signal(M)15.908046
BackgroundAvg:65.16,Std:0.58,Min:63.2,Max:66.5
Spike_AFFX-r2-Ec-bioC_avg-signal270.556793
Spike_AFFX-r2-Bs-dap_avg-signal115.706062
Spike_AFFX-r2-Bs-dap_3-5-ratio2.114591
Spike_AFFX-r2-Ec-bioB_5_signal86.126793
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.742056
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-36_arf7/19_0mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-36_arf7/19_0mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-36_arf7/19_0mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.687004
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.182911
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.188838
Spike_AFFX-r2-Bs-dap_5_signal48.907116
NoiseAvg:2.71,Std:0.07,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.332420
#P13382
Spike_AFFX-r2-Bs-phe_M_signal18.638226
Corner-Avg:10285,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.144005
Spike_AFFX-r2-Ec-bioB_3_signal66.131546
Spike_AFFX-r2-Bs-lys_M_signal6.199646
Spike_AFFX-r2-P1-cre_3_signal3394.757568
Spike_AFFX-r2-Bs-lys_3-5-ratio1.843860
Spike_AFFX-r2-Bs-dap_M_signal96.380783
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.549068
Spike_AFFX-r2-Ec-bioB_avg-signal68.300865
Spike_AFFX-r2-Bs-thr_avg-signal41.209496
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal710.101868
Spike_AFFX-r2-Bs-phe_5_signal24.229876
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1102.655884
RawQ2.342362
Spike_AFFX-r2-Bs-lys_5_signal8.528543
Signal(A)4.778476
%A39.530907
Signal(All)147.819946
Corner+Avg:122,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.918152
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.203600
Spike_AFFX-r2-Ec-bioD_avg-signal906.378906
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.667252
Spike_AFFX-r2-Bs-lys_avg-signal10.151210
Spike_AFFX-r2-P1-cre_avg-signal3132.294922
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.801841
Spike_AFFX-r2-Bs-thr_3_signal69.748230
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.690567
Spike_AFFX-r2-Bs-dap_3_signal106.478348
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.552814
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal190.078049
#M411
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.725438
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.204338
Spike_AFFX-r2-Bs-thr_M_signal38.547832
Signal(P)248.193115
Spike_AFFX-r2-Bs-phe_3-5-ratio0.916373
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8107,Count:9
Spike_AFFX-r2-P1-cre_5_signal2869.832520
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9017
Signal(M)17.920582
BackgroundAvg:63.78,Std:0.45,Min:62.8,Max:65.6
Spike_AFFX-r2-Ec-bioC_avg-signal209.498108
Spike_AFFX-r2-Bs-dap_avg-signal83.922081
Spike_AFFX-r2-Bs-dap_3-5-ratio2.177155
Spike_AFFX-r2-Ec-bioB_5_signal55.627056
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.687004
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-37_arf7/19_15mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-37_arf7/19_15mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-37_arf7/19_15mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.469894
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.239570
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.059121
Spike_AFFX-r2-Bs-dap_5_signal73.844978
NoiseAvg:2.74,Std:0.06,Min:2.6,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.951281
#P14134
Spike_AFFX-r2-Bs-phe_M_signal21.156902
Corner-Avg:7553,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.297134
Spike_AFFX-r2-Ec-bioB_3_signal53.292789
Spike_AFFX-r2-Bs-lys_M_signal15.841328
Spike_AFFX-r2-P1-cre_3_signal3413.539795
Spike_AFFX-r2-Bs-lys_3-5-ratio1.747230
Spike_AFFX-r2-Bs-dap_M_signal140.120529
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.456833
Spike_AFFX-r2-Ec-bioB_avg-signal59.302624
Spike_AFFX-r2-Bs-thr_avg-signal45.075108
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal674.679199
Spike_AFFX-r2-Bs-phe_5_signal28.413723
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal933.708191
RawQ2.400349
Spike_AFFX-r2-Bs-lys_5_signal12.123190
Signal(A)3.217102
%A36.462078
Signal(All)144.264145
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal212.212143
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.072063
Spike_AFFX-r2-Ec-bioD_avg-signal804.193726
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.964050
Spike_AFFX-r2-Bs-lys_avg-signal16.382174
Spike_AFFX-r2-P1-cre_avg-signal3083.675293
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.573871
Spike_AFFX-r2-Bs-thr_3_signal65.511406
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.214228
Spike_AFFX-r2-Bs-dap_3_signal207.664597
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.383929
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal210.923676
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.182001
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.006109
Spike_AFFX-r2-Bs-thr_M_signal50.762638
Signal(P)230.624603
Spike_AFFX-r2-Bs-phe_3-5-ratio1.128753
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4940,Count:9
Spike_AFFX-r2-P1-cre_5_signal2753.810547
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8317
Signal(M)11.866770
BackgroundAvg:59.72,Std:0.45,Min:58.2,Max:61.0
Spike_AFFX-r2-Ec-bioC_avg-signal211.567902
Spike_AFFX-r2-Bs-dap_avg-signal140.543365
Spike_AFFX-r2-Bs-dap_3-5-ratio2.812170
Spike_AFFX-r2-Ec-bioB_5_signal50.317947
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.469894
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-38_arf7/19_30mins_Rep2_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-38_arf7/19_30mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-38_arf7/19_30mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.593524
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.006006
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.909903
Spike_AFFX-r2-Bs-dap_5_signal60.795227
NoiseAvg:2.79,Std:0.13,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.850513
#P13780
Spike_AFFX-r2-Bs-phe_M_signal13.901909
Corner-Avg:6247,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.080513
Spike_AFFX-r2-Ec-bioB_3_signal60.139885
Spike_AFFX-r2-Bs-lys_M_signal8.651513
Spike_AFFX-r2-P1-cre_3_signal3388.006836
Spike_AFFX-r2-Bs-lys_3-5-ratio1.909586
Spike_AFFX-r2-Bs-dap_M_signal109.668007
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.170232
Spike_AFFX-r2-Ec-bioB_avg-signal71.438416
Spike_AFFX-r2-Bs-thr_avg-signal40.227955
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal588.382690
Spike_AFFX-r2-Bs-phe_5_signal24.753056
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal993.195251
RawQ2.523364
Spike_AFFX-r2-Bs-lys_5_signal12.587360
Signal(A)3.712813
%A38.009644
Signal(All)147.412888
Corner+Avg:93,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal221.238724
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.440449
Spike_AFFX-r2-Ec-bioD_avg-signal790.788940
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.412102
Spike_AFFX-r2-Bs-lys_avg-signal15.091842
Spike_AFFX-r2-P1-cre_avg-signal3377.892822
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal45.250454
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.365137
Spike_AFFX-r2-Bs-dap_3_signal170.418945
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.688009
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal214.539017
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.036650
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.031228
Spike_AFFX-r2-Bs-thr_M_signal54.582901
Signal(P)241.315704
Spike_AFFX-r2-Bs-phe_3-5-ratio0.785376
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5434,Count:9
Spike_AFFX-r2-P1-cre_5_signal3367.778809
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8670
Signal(M)13.798437
BackgroundAvg:64.91,Std:0.67,Min:63.7,Max:67.5
Spike_AFFX-r2-Ec-bioC_avg-signal217.888870
Spike_AFFX-r2-Bs-dap_avg-signal113.627388
Spike_AFFX-r2-Bs-dap_3-5-ratio2.803163
Spike_AFFX-r2-Ec-bioB_5_signal66.094849
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.593524
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-39_arf7/19_60mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-39_arf7/19_60mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-39_arf7/19_60mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.516922
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.156265
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.954238
Spike_AFFX-r2-Bs-dap_5_signal101.994484
NoiseAvg:2.52,Std:0.05,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal27.547792
#P14229
Spike_AFFX-r2-Bs-phe_M_signal26.289370
Corner-Avg:6835,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.673409
Spike_AFFX-r2-Ec-bioB_3_signal61.622456
Spike_AFFX-r2-Bs-lys_M_signal24.167482
Spike_AFFX-r2-P1-cre_3_signal4017.914551
Spike_AFFX-r2-Bs-lys_3-5-ratio1.695037
Spike_AFFX-r2-Bs-dap_M_signal186.983673
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.291927
Spike_AFFX-r2-Ec-bioB_avg-signal68.957840
Spike_AFFX-r2-Bs-thr_avg-signal48.259460
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal628.074768
Spike_AFFX-r2-Bs-phe_5_signal22.013744
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal858.839478
RawQ2.331930
Spike_AFFX-r2-Bs-lys_5_signal14.929133
Signal(A)3.169466
%A35.922840
Signal(All)143.876480
Corner+Avg:95,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal240.876312
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.584658
Spike_AFFX-r2-Ec-bioD_avg-signal743.457153
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.380535
Spike_AFFX-r2-Bs-lys_avg-signal21.467346
Spike_AFFX-r2-P1-cre_avg-signal3746.410645
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.696624
Spike_AFFX-r2-Bs-thr_3_signal63.137520
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal24.295923
Spike_AFFX-r2-Bs-dap_3_signal256.700745
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.367416
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal214.565704
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.305426
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.122623
Spike_AFFX-r2-Bs-thr_M_signal54.093063
Signal(P)228.471603
Spike_AFFX-r2-Bs-phe_3-5-ratio1.116787
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4902,Count:9
Spike_AFFX-r2-P1-cre_5_signal3474.906738
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8194
Signal(M)12.737518
BackgroundAvg:58.67,Std:0.71,Min:56.3,Max:60.1
Spike_AFFX-r2-Ec-bioC_avg-signal227.721008
Spike_AFFX-r2-Bs-dap_avg-signal181.892960
Spike_AFFX-r2-Bs-dap_3-5-ratio2.516810
Spike_AFFX-r2-Ec-bioB_5_signal64.577652
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.516922
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-40_arf7/19_120mins_Rep2_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-40_arf7/19_120mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-40_arf7/19_120mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.743349
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.964410
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.023106
Spike_AFFX-r2-Bs-dap_5_signal50.880287
NoiseAvg:2.81,Std:0.09,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.517343
#P13220
Spike_AFFX-r2-Bs-phe_M_signal11.587798
Corner-Avg:6821,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal97.865921
Spike_AFFX-r2-Ec-bioB_3_signal64.558960
Spike_AFFX-r2-Bs-lys_M_signal6.849330
Spike_AFFX-r2-P1-cre_3_signal3513.799316
Spike_AFFX-r2-Bs-lys_3-5-ratio2.274392
Spike_AFFX-r2-Bs-dap_M_signal93.437195
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.407696
Spike_AFFX-r2-Ec-bioB_avg-signal75.175278
Spike_AFFX-r2-Bs-thr_avg-signal39.323246
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal643.477600
Spike_AFFX-r2-Bs-phe_5_signal19.534273
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal988.208252
RawQ2.621044
Spike_AFFX-r2-Bs-lys_5_signal8.008911
Signal(A)4.487072
%A40.398949
Signal(All)151.925461
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal263.844421
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.870865
Spike_AFFX-r2-Ec-bioD_avg-signal815.842896
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.957035
Spike_AFFX-r2-Bs-lys_avg-signal11.024549
Spike_AFFX-r2-P1-cre_avg-signal3578.634766
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.644016
Spike_AFFX-r2-Bs-thr_3_signal62.282288
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.330978
Spike_AFFX-r2-Bs-dap_3_signal111.580406
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.535731
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal251.462616
#M375
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.215403
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.049239
Spike_AFFX-r2-Bs-thr_M_signal44.170101
Signal(P)258.525269
Spike_AFFX-r2-Bs-phe_3-5-ratio1.068423
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4431,Count:9
Spike_AFFX-r2-P1-cre_5_signal3643.470215
Spike_AFFX-r2-Bs-phe_M_detectionM
#A9215
Signal(M)16.979698
BackgroundAvg:66.77,Std:0.50,Min:65.6,Max:68.0
Spike_AFFX-r2-Ec-bioC_avg-signal257.653503
Spike_AFFX-r2-Bs-dap_avg-signal85.299294
Spike_AFFX-r2-Bs-dap_3-5-ratio2.192999
Spike_AFFX-r2-Ec-bioB_5_signal63.100952
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.743349
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-41_arf7/19_240mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-41_arf7/19_240mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-41_arf7/19_240mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.583901
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.960653
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.028793
Spike_AFFX-r2-Bs-dap_5_signal46.941982
NoiseAvg:2.82,Std:0.08,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.034519
#P13534
Spike_AFFX-r2-Bs-phe_M_signal20.040682
Corner-Avg:6559,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.800316
Spike_AFFX-r2-Ec-bioB_3_signal57.507603
Spike_AFFX-r2-Bs-lys_M_signal6.347480
Spike_AFFX-r2-P1-cre_3_signal3252.657715
Spike_AFFX-r2-Bs-lys_3-5-ratio3.282112
Spike_AFFX-r2-Bs-dap_M_signal93.942604
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.088759
Spike_AFFX-r2-Ec-bioB_avg-signal63.735340
Spike_AFFX-r2-Bs-thr_avg-signal30.616669
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal687.926392
Spike_AFFX-r2-Bs-phe_5_signal18.688166
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1086.835205
RawQ2.607269
Spike_AFFX-r2-Bs-lys_5_signal9.904905
Signal(A)4.002832
%A39.083736
Signal(All)148.939484
Corner+Avg:94,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal229.125702
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.190403
Spike_AFFX-r2-Ec-bioD_avg-signal887.380798
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.333626
Spike_AFFX-r2-Bs-lys_avg-signal16.253798
Spike_AFFX-r2-P1-cre_avg-signal3319.270020
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.582639
Spike_AFFX-r2-Bs-thr_3_signal35.581001
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.306417
Spike_AFFX-r2-Bs-dap_3_signal147.686081
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.579871
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.326523
#M361
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.509007
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.059166
Spike_AFFX-r2-Bs-thr_M_signal39.234482
Signal(P)247.965454
Spike_AFFX-r2-Bs-phe_3-5-ratio0.866345
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4648,Count:9
Spike_AFFX-r2-P1-cre_5_signal3385.882324
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8915
Signal(M)15.678021
BackgroundAvg:68.41,Std:0.44,Min:67.1,Max:70.0
Spike_AFFX-r2-Ec-bioC_avg-signal222.726105
Spike_AFFX-r2-Bs-dap_avg-signal96.190224
Spike_AFFX-r2-Bs-dap_3-5-ratio3.146141
Spike_AFFX-r2-Ec-bioB_5_signal55.898109
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.583901
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-42_arf7/19_480mins_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-42_arf7/19_480mins_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-42_arf7/19_480mins_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.667031
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.188133
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.976019
Spike_AFFX-r2-Bs-dap_5_signal103.504578
NoiseAvg:2.40,Std:0.10,Min:2.1,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.849514
#P13924
Spike_AFFX-r2-Bs-phe_M_signal21.439096
Corner-Avg:7085,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.256279
Spike_AFFX-r2-Ec-bioB_3_signal72.000710
Spike_AFFX-r2-Bs-lys_M_signal14.576247
Spike_AFFX-r2-P1-cre_3_signal4671.689941
Spike_AFFX-r2-Bs-lys_3-5-ratio0.994541
Spike_AFFX-r2-Bs-dap_M_signal162.266083
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.433512
Spike_AFFX-r2-Ec-bioB_avg-signal82.675598
Spike_AFFX-r2-Bs-thr_avg-signal44.883106
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal740.221252
Spike_AFFX-r2-Bs-phe_5_signal27.671366
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1109.269165
RawQ2.286444
Spike_AFFX-r2-Bs-lys_5_signal19.950512
Signal(A)3.760197
%A37.387112
Signal(All)148.803299
Corner+Avg:90,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal286.432861
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.991611
Spike_AFFX-r2-Ec-bioD_avg-signal924.745239
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.043404
Spike_AFFX-r2-Bs-lys_avg-signal18.122786
Spike_AFFX-r2-P1-cre_avg-signal4301.824219
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.569487
Spike_AFFX-r2-Bs-thr_3_signal53.171062
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.034025
Spike_AFFX-r2-Bs-dap_3_signal237.773361
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.498564
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal275.004547
#M358
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.841600
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.041557
Spike_AFFX-r2-Bs-thr_M_signal59.628742
Signal(P)241.089981
Spike_AFFX-r2-Bs-phe_3-5-ratio1.047712
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5341,Count:9
Spike_AFFX-r2-P1-cre_5_signal3931.958984
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8528
Signal(M)14.523555
BackgroundAvg:58.04,Std:0.35,Min:57.0,Max:58.7
Spike_AFFX-r2-Ec-bioC_avg-signal280.718689
Spike_AFFX-r2-Bs-dap_avg-signal167.848007
Spike_AFFX-r2-Bs-dap_3-5-ratio2.297225
Spike_AFFX-r2-Ec-bioB_5_signal73.769806
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.667031
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-43_arf7/19_0mins_Rep3_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-43_arf7/19_0mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-43_arf7/19_0mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.658704
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.218753
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.037903
Spike_AFFX-r2-Bs-dap_5_signal60.331867
NoiseAvg:2.86,Std:0.09,Min:2.7,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.459827
#P13365
Spike_AFFX-r2-Bs-phe_M_signal20.049002
Corner-Avg:7027,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.347313
Spike_AFFX-r2-Ec-bioB_3_signal58.561573
Spike_AFFX-r2-Bs-lys_M_signal11.849885
Spike_AFFX-r2-P1-cre_3_signal3477.760254
Spike_AFFX-r2-Bs-lys_3-5-ratio1.188997
Spike_AFFX-r2-Bs-dap_M_signal122.066368
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.139381
Spike_AFFX-r2-Ec-bioB_avg-signal63.443951
Spike_AFFX-r2-Bs-thr_avg-signal36.176620
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal636.697998
Spike_AFFX-r2-Bs-phe_5_signal21.767456
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal988.094666
RawQ2.631584
Spike_AFFX-r2-Bs-lys_5_signal20.249805
Signal(A)4.033661
%A39.736958
Signal(All)148.855743
Corner+Avg:102,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal212.752350
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.172382
Spike_AFFX-r2-Ec-bioD_avg-signal812.396362
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.592724
Spike_AFFX-r2-Bs-lys_avg-signal18.725548
Spike_AFFX-r2-P1-cre_avg-signal3165.650391
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.670320
Spike_AFFX-r2-Bs-thr_3_signal51.673676
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal24.662947
Spike_AFFX-r2-Bs-dap_3_signal168.841156
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.551905
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal217.969360
#M381
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.076954
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.976065
Spike_AFFX-r2-Bs-thr_M_signal40.396362
Signal(P)250.868973
Spike_AFFX-r2-Bs-phe_3-5-ratio1.478004
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4931,Count:9
Spike_AFFX-r2-P1-cre_5_signal2853.540771
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9064
Signal(M)15.681962
BackgroundAvg:68.34,Std:0.55,Min:67.2,Max:70.2
Spike_AFFX-r2-Ec-bioC_avg-signal215.360855
Spike_AFFX-r2-Bs-dap_avg-signal117.079803
Spike_AFFX-r2-Bs-dap_3-5-ratio2.798540
Spike_AFFX-r2-Ec-bioB_5_signal56.422966
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.658704
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-44_arf7/19_15mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-44_arf7/19_15mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-44_arf7/19_15mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.502457
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.081744
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.992887
Spike_AFFX-r2-Bs-dap_5_signal48.633198
NoiseAvg:3.01,Std:0.09,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.322179
#P13572
Spike_AFFX-r2-Bs-phe_M_signal13.690981
Corner-Avg:6988,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.777306
Spike_AFFX-r2-Ec-bioB_3_signal48.439285
Spike_AFFX-r2-Bs-lys_M_signal9.033638
Spike_AFFX-r2-P1-cre_3_signal3328.162842
Spike_AFFX-r2-Bs-lys_3-5-ratio2.222785
Spike_AFFX-r2-Bs-dap_M_signal88.254974
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.984684
Spike_AFFX-r2-Ec-bioB_avg-signal59.334290
Spike_AFFX-r2-Bs-thr_avg-signal31.273268
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal662.939453
Spike_AFFX-r2-Bs-phe_5_signal14.677489
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1000.481323
RawQ2.671019
Spike_AFFX-r2-Bs-lys_5_signal12.716732
Signal(A)3.949599
%A38.711090
Signal(All)146.881699
Corner+Avg:102,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal200.060425
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.064144
Spike_AFFX-r2-Ec-bioD_avg-signal831.710388
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P59.500217
Spike_AFFX-r2-Bs-lys_avg-signal16.672312
Spike_AFFX-r2-P1-cre_avg-signal3202.413086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.788689
Spike_AFFX-r2-Bs-thr_3_signal46.468109
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal15.477538
Spike_AFFX-r2-Bs-dap_3_signal127.297005
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.509159
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal214.411011
#M408
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.266563
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.933070
Spike_AFFX-r2-Bs-thr_M_signal38.029510
Signal(P)243.795181
Spike_AFFX-r2-Bs-phe_3-5-ratio1.230738
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4740,Count:9
Spike_AFFX-r2-P1-cre_5_signal3076.663086
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8830
Signal(M)16.442175
BackgroundAvg:68.32,Std:0.39,Min:67.4,Max:69.5
Spike_AFFX-r2-Ec-bioC_avg-signal207.235718
Spike_AFFX-r2-Bs-dap_avg-signal88.061729
Spike_AFFX-r2-Bs-dap_3-5-ratio2.617492
Spike_AFFX-r2-Ec-bioB_5_signal48.786289
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.502457
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-45_arf7/19_30mins_Rep3_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-45_arf7/19_30mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-45_arf7/19_30mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.592381
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.158382
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.014383
Spike_AFFX-r2-Bs-dap_5_signal77.832283
NoiseAvg:2.41,Std:0.06,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.177490
#P13947
Spike_AFFX-r2-Bs-phe_M_signal30.433474
Corner-Avg:8101,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal106.090797
Spike_AFFX-r2-Ec-bioB_3_signal66.131668
Spike_AFFX-r2-Bs-lys_M_signal23.128368
Spike_AFFX-r2-P1-cre_3_signal4040.707275
Spike_AFFX-r2-Bs-lys_3-5-ratio1.223545
Spike_AFFX-r2-Bs-dap_M_signal184.659576
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.557176
Spike_AFFX-r2-Ec-bioB_avg-signal79.138817
Spike_AFFX-r2-Bs-thr_avg-signal55.556194
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal830.252563
Spike_AFFX-r2-Bs-phe_5_signal27.339355
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1238.892456
RawQ2.176272
Spike_AFFX-r2-Bs-lys_5_signal16.645815
Signal(A)3.441603
%A37.264359
Signal(All)144.527267
Corner+Avg:110,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal301.284393
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.349503
Spike_AFFX-r2-Ec-bioD_avg-signal1034.572510
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.144234
Spike_AFFX-r2-Bs-lys_avg-signal20.047028
Spike_AFFX-r2-P1-cre_avg-signal3764.471191
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal86.003586
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal30.707443
Spike_AFFX-r2-Bs-dap_3_signal256.160919
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.492188
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal302.517517
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.366901
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.995924
Spike_AFFX-r2-Bs-thr_M_signal56.487511
Signal(P)233.916016
Spike_AFFX-r2-Bs-phe_3-5-ratio1.256412
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4795,Count:9
Spike_AFFX-r2-P1-cre_5_signal3488.234863
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8500
Signal(M)13.737469
BackgroundAvg:54.34,Std:0.53,Min:53.4,Max:56.2
Spike_AFFX-r2-Ec-bioC_avg-signal301.900940
Spike_AFFX-r2-Bs-dap_avg-signal172.884262
Spike_AFFX-r2-Bs-dap_3-5-ratio3.291191
Spike_AFFX-r2-Ec-bioB_5_signal65.193970
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.592381
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-46_arf7/19_60mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-46_arf7/19_60mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-46_arf7/19_60mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.534598
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.924167
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.252677
Spike_AFFX-r2-Bs-dap_5_signal43.012203
NoiseAvg:2.74,Std:0.11,Min:2.5,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.776757
#P13798
Spike_AFFX-r2-Bs-phe_M_signal9.782339
Corner-Avg:8159,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.964600
Spike_AFFX-r2-Ec-bioB_3_signal59.286137
Spike_AFFX-r2-Bs-lys_M_signal12.960169
Spike_AFFX-r2-P1-cre_3_signal3016.632324
Spike_AFFX-r2-Bs-lys_3-5-ratio3.291636
Spike_AFFX-r2-Bs-dap_M_signal94.845284
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.440654
Spike_AFFX-r2-Ec-bioB_avg-signal62.859432
Spike_AFFX-r2-Bs-thr_avg-signal29.772890
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal651.783142
Spike_AFFX-r2-Bs-phe_5_signal14.450505
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal960.814514
RawQ2.555453
Spike_AFFX-r2-Bs-lys_5_signal8.016726
Signal(A)3.213777
%A38.027180
Signal(All)145.054092
Corner+Avg:118,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal240.220139
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.422447
Spike_AFFX-r2-Ec-bioD_avg-signal806.298828
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.491013
Spike_AFFX-r2-Bs-lys_avg-signal15.788345
Spike_AFFX-r2-P1-cre_avg-signal3140.398926
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal38.505604
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal14.885098
Spike_AFFX-r2-Bs-dap_3_signal123.164192
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.474132
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal247.778519
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.388145
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.969495
Spike_AFFX-r2-Bs-thr_M_signal35.036308
Signal(P)237.439957
Spike_AFFX-r2-Bs-phe_3-5-ratio1.413269
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5361,Count:9
Spike_AFFX-r2-P1-cre_5_signal3264.165283
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8674
Signal(M)13.641973
BackgroundAvg:65.75,Std:0.31,Min:65.0,Max:67.0
Spike_AFFX-r2-Ec-bioC_avg-signal243.999329
Spike_AFFX-r2-Bs-dap_avg-signal87.007225
Spike_AFFX-r2-Bs-dap_3-5-ratio2.863471
Spike_AFFX-r2-Ec-bioB_5_signal47.327564
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.534598
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-47_arf7/19_120mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-47_arf7/19_120mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-47_arf7/19_120mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.582178
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.130871
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.803045
Spike_AFFX-r2-Bs-dap_5_signal33.935482
NoiseAvg:2.28,Std:0.04,Min:2.2,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.044400
#P13995
Spike_AFFX-r2-Bs-phe_M_signal11.849830
Corner-Avg:7243,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal107.737747
Spike_AFFX-r2-Ec-bioB_3_signal76.224335
Spike_AFFX-r2-Bs-lys_M_signal11.856262
Spike_AFFX-r2-P1-cre_3_signal4776.916016
Spike_AFFX-r2-Bs-lys_3-5-ratio1.650522
Spike_AFFX-r2-Bs-dap_M_signal94.377251
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.956023
Spike_AFFX-r2-Ec-bioB_avg-signal92.960388
Spike_AFFX-r2-Bs-thr_avg-signal38.340328
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal839.050659
Spike_AFFX-r2-Bs-phe_5_signal18.956520
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1235.040771
RawQ2.251947
Spike_AFFX-r2-Bs-lys_5_signal11.873071
Signal(A)3.003968
%A37.220516
Signal(All)146.596863
Corner+Avg:93,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal347.007690
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.583395
Spike_AFFX-r2-Ec-bioD_avg-signal1037.045654
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.354668
Spike_AFFX-r2-Bs-lys_avg-signal14.442035
Spike_AFFX-r2-P1-cre_avg-signal4500.510254
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.424814
Spike_AFFX-r2-Bs-thr_3_signal71.736725
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.796581
Spike_AFFX-r2-Bs-dap_3_signal173.164108
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.471950
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal317.346161
#M325
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.596769
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.093467
Spike_AFFX-r2-Bs-thr_M_signal31.239855
Signal(P)236.822708
Spike_AFFX-r2-Bs-phe_3-5-ratio1.191326
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5956,Count:9
Spike_AFFX-r2-P1-cre_5_signal4224.104492
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8490
Signal(M)12.421643
BackgroundAvg:54.59,Std:0.62,Min:53.1,Max:56.5
Spike_AFFX-r2-Ec-bioC_avg-signal332.176941
Spike_AFFX-r2-Bs-dap_avg-signal100.492279
Spike_AFFX-r2-Bs-dap_3-5-ratio5.102745
Spike_AFFX-r2-Ec-bioB_5_signal94.919098
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.582178
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-48_arf7/19_240mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-48_arf7/19_240mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-48_arf7/19_240mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.542019
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.077445
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.817880
Spike_AFFX-r2-Bs-dap_5_signal47.521408
NoiseAvg:2.55,Std:0.09,Min:2.3,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.625463
#P13854
Spike_AFFX-r2-Bs-phe_M_signal17.365824
Corner-Avg:7413,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.051926
Spike_AFFX-r2-Ec-bioB_3_signal64.747887
Spike_AFFX-r2-Bs-lys_M_signal9.794706
Spike_AFFX-r2-P1-cre_3_signal3873.484863
Spike_AFFX-r2-Bs-lys_3-5-ratio1.505061
Spike_AFFX-r2-Bs-dap_M_signal145.858063
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.271420
Spike_AFFX-r2-Ec-bioB_avg-signal81.988457
Spike_AFFX-r2-Bs-thr_avg-signal39.918011
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal801.293396
Spike_AFFX-r2-Bs-phe_5_signal19.295126
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1153.176880
RawQ2.279438
Spike_AFFX-r2-Bs-lys_5_signal13.612153
Signal(A)3.293814
%A37.781673
Signal(All)146.587692
Corner+Avg:97,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal263.306580
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.811909
Spike_AFFX-r2-Ec-bioD_avg-signal977.235107
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.736519
Spike_AFFX-r2-Bs-lys_avg-signal14.631328
Spike_AFFX-r2-P1-cre_avg-signal3734.274658
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal51.117455
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.490953
Spike_AFFX-r2-Bs-dap_3_signal208.436417
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.439144
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal261.044586
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.487123
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.008665
Spike_AFFX-r2-Bs-thr_M_signal53.011108
Signal(P)238.961533
Spike_AFFX-r2-Bs-phe_3-5-ratio1.441396
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6301,Count:9
Spike_AFFX-r2-P1-cre_5_signal3595.064453
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8618
Signal(M)13.923744
BackgroundAvg:59.99,Std:0.58,Min:58.4,Max:61.7
Spike_AFFX-r2-Ec-bioC_avg-signal262.175598
Spike_AFFX-r2-Bs-dap_avg-signal133.938644
Spike_AFFX-r2-Bs-dap_3-5-ratio4.386158
Spike_AFFX-r2-Ec-bioB_5_signal79.165550
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.542019
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-49_arf7/19_480mins_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-49_arf7/19_480mins_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-49_arf7/19_480mins_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.631851
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.759558
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.114568
Spike_AFFX-r2-Bs-dap_5_signal39.230457
NoiseAvg:2.21,Std:0.08,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.047080
#P13906
Spike_AFFX-r2-Bs-phe_M_signal12.339060
Corner-Avg:8156,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal122.088058
Spike_AFFX-r2-Ec-bioB_3_signal83.342018
Spike_AFFX-r2-Bs-lys_M_signal10.102084
Spike_AFFX-r2-P1-cre_3_signal3367.777344
Spike_AFFX-r2-Bs-lys_3-5-ratio1.275917
Spike_AFFX-r2-Bs-dap_M_signal85.707855
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.515637
Spike_AFFX-r2-Ec-bioB_avg-signal93.401741
Spike_AFFX-r2-Bs-thr_avg-signal27.759806
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal822.123718
Spike_AFFX-r2-Bs-phe_5_signal27.290113
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1410.586426
RawQ2.201525
Spike_AFFX-r2-Bs-lys_5_signal14.748839
Signal(A)3.081031
%A37.430950
Signal(All)147.424042
Corner+Avg:101,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal306.208344
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.588524
Spike_AFFX-r2-Ec-bioD_avg-signal1116.355103
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.964489
Spike_AFFX-r2-Bs-lys_avg-signal14.556408
Spike_AFFX-r2-P1-cre_avg-signal3900.822021
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal45.916210
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.405899
Spike_AFFX-r2-Bs-dap_3_signal167.526657
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.715784
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal312.776520
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.818300
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.979000
Spike_AFFX-r2-Bs-thr_M_signal30.316128
Signal(P)239.600418
Spike_AFFX-r2-Bs-phe_3-5-ratio0.791075
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5826,Count:9
Spike_AFFX-r2-P1-cre_5_signal4433.866699
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8538
Signal(M)12.440483
BackgroundAvg:55.13,Std:0.37,Min:54.3,Max:56.4
Spike_AFFX-r2-Ec-bioC_avg-signal309.492432
Spike_AFFX-r2-Bs-dap_avg-signal97.488319
Spike_AFFX-r2-Bs-dap_3-5-ratio4.270321
Spike_AFFX-r2-Ec-bioB_5_signal74.775154
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.631851
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-50_arf7/19_0mins_Rep4_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-50_arf7/19_0mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-50_arf7/19_0mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.623414
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.137644
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.825911
Spike_AFFX-r2-Bs-dap_5_signal95.419670
NoiseAvg:2.37,Std:0.06,Min:2.0,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.262325
#P14026
Spike_AFFX-r2-Bs-phe_M_signal18.998959
Corner-Avg:8357,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal101.866478
Spike_AFFX-r2-Ec-bioB_3_signal77.151726
Spike_AFFX-r2-Bs-lys_M_signal11.124047
Spike_AFFX-r2-P1-cre_3_signal4750.912109
Spike_AFFX-r2-Bs-lys_3-5-ratio2.089688
Spike_AFFX-r2-Bs-dap_M_signal135.997360
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.895717
Spike_AFFX-r2-Ec-bioB_avg-signal90.810783
Spike_AFFX-r2-Bs-thr_avg-signal48.847122
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal793.278625
Spike_AFFX-r2-Bs-phe_5_signal22.758087
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1224.020874
RawQ2.212104
Spike_AFFX-r2-Bs-lys_5_signal12.702846
Signal(A)3.499395
%A36.847874
Signal(All)144.585144
Corner+Avg:102,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal353.804565
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.119671
Spike_AFFX-r2-Ec-bioD_avg-signal1008.649780
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.490574
Spike_AFFX-r2-Bs-lys_avg-signal16.790628
Spike_AFFX-r2-P1-cre_avg-signal4463.505859
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.661552
Spike_AFFX-r2-Bs-thr_3_signal78.936279
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal24.292238
Spike_AFFX-r2-Bs-dap_3_signal199.608032
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.542990
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal290.472961
#M379
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.544989
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.218029
Spike_AFFX-r2-Bs-thr_M_signal47.342766
Signal(P)232.642944
Spike_AFFX-r2-Bs-phe_3-5-ratio1.367411
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5694,Count:9
Spike_AFFX-r2-P1-cre_5_signal4176.099121
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8405
Signal(M)14.577068
BackgroundAvg:57.61,Std:0.24,Min:57.0,Max:58.3
Spike_AFFX-r2-Ec-bioC_avg-signal322.138763
Spike_AFFX-r2-Bs-dap_avg-signal143.675034
Spike_AFFX-r2-Bs-dap_3-5-ratio2.091896
Spike_AFFX-r2-Ec-bioB_5_signal93.414131
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.623414
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-51_arf7/19_15mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-51_arf7/19_15mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-51_arf7/19_15mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.459519
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.041142
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.043596
Spike_AFFX-r2-Bs-dap_5_signal72.447372
NoiseAvg:2.52,Std:0.06,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.713743
#P14346
Spike_AFFX-r2-Bs-phe_M_signal13.410392
Corner-Avg:8930,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.258423
Spike_AFFX-r2-Ec-bioB_3_signal73.164673
Spike_AFFX-r2-Bs-lys_M_signal15.245478
Spike_AFFX-r2-P1-cre_3_signal3818.931152
Spike_AFFX-r2-Bs-lys_3-5-ratio1.489799
Spike_AFFX-r2-Bs-dap_M_signal114.600197
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.501213
Spike_AFFX-r2-Ec-bioB_avg-signal78.177116
Spike_AFFX-r2-Bs-thr_avg-signal33.624165
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal670.291077
Spike_AFFX-r2-Bs-phe_5_signal19.120960
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal963.281311
RawQ2.276914
Spike_AFFX-r2-Bs-lys_5_signal14.308775
Signal(A)2.879913
%A35.598423
Signal(All)141.755417
Corner+Avg:110,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal258.195007
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.716711
Spike_AFFX-r2-Ec-bioD_avg-signal816.786194
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.893467
Spike_AFFX-r2-Bs-lys_avg-signal16.957153
Spike_AFFX-r2-P1-cre_avg-signal3743.476563
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.508111
Spike_AFFX-r2-Bs-thr_3_signal46.807064
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.082687
Spike_AFFX-r2-Bs-dap_3_signal178.005295
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.437109
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal233.732727
#M344
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.317204
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.104659
Spike_AFFX-r2-Bs-thr_M_signal35.351681
Signal(P)223.473175
Spike_AFFX-r2-Bs-phe_3-5-ratio0.978858
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7351,Count:9
Spike_AFFX-r2-P1-cre_5_signal3668.021973
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8120
Signal(M)11.947007
BackgroundAvg:60.00,Std:0.48,Min:58.6,Max:61.4
Spike_AFFX-r2-Ec-bioC_avg-signal245.963867
Spike_AFFX-r2-Bs-dap_avg-signal121.684288
Spike_AFFX-r2-Bs-dap_3-5-ratio2.457029
Spike_AFFX-r2-Ec-bioB_5_signal70.108253
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.459519
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-52_arf7/19_30mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-52_arf7/19_30mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-52_arf7/19_30mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.393958
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.068893
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.827500
Spike_AFFX-r2-Bs-dap_5_signal60.698620
NoiseAvg:3.08,Std:0.08,Min:2.8,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.225101
#P14072
Spike_AFFX-r2-Bs-phe_M_signal16.734547
Corner-Avg:7794,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal69.240112
Spike_AFFX-r2-Ec-bioB_3_signal42.167873
Spike_AFFX-r2-Bs-lys_M_signal14.141057
Spike_AFFX-r2-P1-cre_3_signal2909.751465
Spike_AFFX-r2-Bs-lys_3-5-ratio2.757194
Spike_AFFX-r2-Bs-dap_M_signal99.047028
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.030336
Spike_AFFX-r2-Ec-bioB_avg-signal54.122040
Spike_AFFX-r2-Bs-thr_avg-signal31.348471
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal548.451782
Spike_AFFX-r2-Bs-phe_5_signal23.300522
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal858.578003
RawQ2.682523
Spike_AFFX-r2-Bs-lys_5_signal10.476514
Signal(A)2.908493
%A36.782112
Signal(All)142.135910
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal216.052521
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.402660
Spike_AFFX-r2-Ec-bioD_avg-signal703.514893
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.692242
Spike_AFFX-r2-Bs-lys_avg-signal17.834450
Spike_AFFX-r2-P1-cre_avg-signal2815.980469
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.525647
Spike_AFFX-r2-Bs-thr_3_signal37.003078
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.145910
Spike_AFFX-r2-Bs-dap_3_signal155.795822
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.565458
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal189.581329
#M348
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.885778
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.139630
Spike_AFFX-r2-Bs-thr_M_signal38.817226
Signal(P)228.332062
Spike_AFFX-r2-Bs-phe_3-5-ratio0.746879
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5615,Count:9
Spike_AFFX-r2-P1-cre_5_signal2722.209229
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8390
Signal(M)13.302452
BackgroundAvg:70.15,Std:0.53,Min:68.8,Max:72.3
Spike_AFFX-r2-Ec-bioC_avg-signal202.816925
Spike_AFFX-r2-Bs-dap_avg-signal105.180489
Spike_AFFX-r2-Bs-dap_3-5-ratio2.566711
Spike_AFFX-r2-Ec-bioB_5_signal50.958134
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.393958
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-53_arf7/19_60mins_Rep4_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-53_arf7/19_60mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-53_arf7/19_60mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.499005
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.189802
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.820809
Spike_AFFX-r2-Bs-dap_5_signal80.693535
NoiseAvg:2.59,Std:0.11,Min:2.3,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.518902
#P13955
Spike_AFFX-r2-Bs-phe_M_signal21.320305
Corner-Avg:7886,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.031677
Spike_AFFX-r2-Ec-bioB_3_signal43.813190
Spike_AFFX-r2-Bs-lys_M_signal10.957361
Spike_AFFX-r2-P1-cre_3_signal3592.634521
Spike_AFFX-r2-Bs-lys_3-5-ratio1.178506
Spike_AFFX-r2-Bs-dap_M_signal117.385025
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.248223
Spike_AFFX-r2-Ec-bioB_avg-signal60.740967
Spike_AFFX-r2-Bs-thr_avg-signal45.130306
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal589.035767
Spike_AFFX-r2-Bs-phe_5_signal24.905304
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal878.297852
RawQ2.266536
Spike_AFFX-r2-Bs-lys_5_signal12.233226
Signal(A)3.338778
%A37.316967
Signal(All)144.086288
Corner+Avg:118,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal196.558319
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.443741
Spike_AFFX-r2-Ec-bioD_avg-signal733.666809
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.179306
Spike_AFFX-r2-Bs-lys_avg-signal12.535839
Spike_AFFX-r2-P1-cre_avg-signal3306.079346
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.503726
Spike_AFFX-r2-Bs-thr_3_signal74.424210
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.889784
Spike_AFFX-r2-Bs-dap_3_signal161.098434
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.491077
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal221.238022
#M343
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.416929
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.888447
Spike_AFFX-r2-Bs-thr_M_signal43.447800
Signal(P)233.126923
Spike_AFFX-r2-Bs-phe_3-5-ratio0.780707
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4954,Count:9
Spike_AFFX-r2-P1-cre_5_signal3019.524170
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8512
Signal(M)14.292960
BackgroundAvg:79.85,Std:0.49,Min:78.5,Max:81.2
Spike_AFFX-r2-Ec-bioC_avg-signal208.898163
Spike_AFFX-r2-Bs-dap_avg-signal119.725670
Spike_AFFX-r2-Bs-dap_3-5-ratio1.996423
Spike_AFFX-r2-Ec-bioB_5_signal53.378044
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.499005
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-54_arf7/19_120mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-54_arf7/19_120mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-54_arf7/19_120mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.379087
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.107653
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.799444
Spike_AFFX-r2-Bs-dap_5_signal79.337814
NoiseAvg:2.58,Std:0.25,Min:2.3,Max:4.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.976250
#P14325
Spike_AFFX-r2-Bs-phe_M_signal18.673101
Corner-Avg:8439,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal69.965195
Spike_AFFX-r2-Ec-bioB_3_signal47.674973
Spike_AFFX-r2-Bs-lys_M_signal13.414812
Spike_AFFX-r2-P1-cre_3_signal3075.402588
Spike_AFFX-r2-Bs-lys_3-5-ratio1.399511
Spike_AFFX-r2-Bs-dap_M_signal128.013474
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.259358
Spike_AFFX-r2-Ec-bioB_avg-signal59.091770
Spike_AFFX-r2-Bs-thr_avg-signal36.437870
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal569.851807
Spike_AFFX-r2-Bs-phe_5_signal21.161293
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal809.442078
RawQ2.287888
Spike_AFFX-r2-Bs-lys_5_signal13.888515
Signal(A)2.634239
%A35.712406
Signal(All)139.604294
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.788391
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.535303
Spike_AFFX-r2-Ec-bioD_avg-signal689.646973
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.801403
Spike_AFFX-r2-Bs-lys_avg-signal15.580153
Spike_AFFX-r2-P1-cre_avg-signal2925.953125
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.486190
Spike_AFFX-r2-Bs-thr_3_signal47.392857
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.789900
Spike_AFFX-r2-Bs-dap_3_signal195.315308
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.420443
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal185.769272
#M339
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.437130
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.107763
Spike_AFFX-r2-Bs-thr_M_signal40.944496
Signal(P)220.539307
Spike_AFFX-r2-Bs-phe_3-5-ratio1.348467
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6257,Count:9
Spike_AFFX-r2-P1-cre_5_signal2776.503906
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8146
Signal(M)10.884487
BackgroundAvg:77.71,Std:0.42,Min:76.2,Max:78.7
Spike_AFFX-r2-Ec-bioC_avg-signal195.778839
Spike_AFFX-r2-Bs-dap_avg-signal134.222214
Spike_AFFX-r2-Bs-dap_3-5-ratio2.461819
Spike_AFFX-r2-Ec-bioB_5_signal59.635151
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.379087
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-55_arf7/19_240mins_Rep4_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-55_arf7/19_240mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-55_arf7/19_240mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.466487
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.101723
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.987253
Spike_AFFX-r2-Bs-dap_5_signal73.446068
NoiseAvg:2.57,Std:0.05,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.073633
#P13801
Spike_AFFX-r2-Bs-phe_M_signal15.823715
Corner-Avg:7487,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.623428
Spike_AFFX-r2-Ec-bioB_3_signal65.591667
Spike_AFFX-r2-Bs-lys_M_signal10.832023
Spike_AFFX-r2-P1-cre_3_signal3745.505127
Spike_AFFX-r2-Bs-lys_3-5-ratio1.615041
Spike_AFFX-r2-Bs-dap_M_signal117.529358
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.904776
Spike_AFFX-r2-Ec-bioB_avg-signal74.884552
Spike_AFFX-r2-Bs-thr_avg-signal31.069138
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal762.403564
Spike_AFFX-r2-Bs-phe_5_signal23.626682
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1049.842285
RawQ2.260026
Spike_AFFX-r2-Bs-lys_5_signal12.396978
Signal(A)3.119900
%A38.000877
Signal(All)145.417175
Corner+Avg:100,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal276.078003
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.765104
Spike_AFFX-r2-Ec-bioD_avg-signal906.122925
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.504166
Spike_AFFX-r2-Bs-lys_avg-signal14.416878
Spike_AFFX-r2-P1-cre_avg-signal3572.591797
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.494958
Spike_AFFX-r2-Bs-thr_3_signal42.045334
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.738501
Spike_AFFX-r2-Bs-dap_3_signal161.058456
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.377017
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal228.452011
#M341
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.021629
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.208473
Spike_AFFX-r2-Bs-thr_M_signal29.088448
Signal(P)238.052094
Spike_AFFX-r2-Bs-phe_3-5-ratio0.836559
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5980,Count:9
Spike_AFFX-r2-P1-cre_5_signal3399.678711
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8668
Signal(M)13.388754
BackgroundAvg:81.54,Std:0.58,Min:79.8,Max:83.2
Spike_AFFX-r2-Ec-bioC_avg-signal252.265015
Spike_AFFX-r2-Bs-dap_avg-signal117.344635
Spike_AFFX-r2-Bs-dap_3-5-ratio2.192881
Spike_AFFX-r2-Ec-bioB_5_signal66.438568
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.466487
NF1.000000
HZ4
Tau0.015000

Slide: Mendocilla Sato_546-56_arf7/19_480mins_Rep4_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Mendocilla Sato_546-56_arf7/19_480mins_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Mendocilla Sato_546-56_arf7/19_480mins_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: arf7/19
Stock Code:
Age: 7 days old
Growth Conditions:
Stratification3 days, 4 C, dark
SterilisationSterilisation seed protocol: • Place seeds into a 1.5 ml Eppendorf tube. • Add 1 ml 5% (v/v) bleach in sterile water for five minutes, inverting the tube periodically in order to wet all the seeds. • Remove the bleach and add 1 ml sterile water. Invert the tube to mix. Remove the water. • Repeat the rinse three times, leaving the seeds in the final rinse.
ProtocolGrowth protocol: Sterilised 100 um nylon mesh was placed onto the surface of half-strength Murashige Skoog (MS) plus 1% (w/v) of agarose before plating the seeds. Arabidopsis thaliana seeds were surface sterilised and plated onto 12 cm square petri-dishes containing the media mentioned below. Thirty seeds were placed diagonally across the nylon mesh so roots don’t mix each other when applying the gravity stimulation. After incubation at 4°C for 3 days in the dark (stratification protocol), plates were transferred to the controlled environment growth room (23°C, 150 µmol m-2 s-1, and continuous light) for 7 days. Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes). The dissection of wild-type and arf7arf19 double mutant seedlings was done under a light microscope.
Plant Spacing30 seedlings/12cm plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: Cool white fluorescent. Intensity: 150 µmol m-2 s-1µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: primary root tips
in vivo Treatment: Seven-day old seedlings were gravity stimulated by 90° reorientation. Zones 1 and 2 were harvested over a time-course ranging from 0 minutes up to 8 hours (0,15, 30, 60, 120, 240 and 480 minutes).
Additional Organism Information:
Sample DescriptionRoot dissection of zones 1 (meristem) and zone 2 (accelerating elongation zone)
Other Information:
Timecourse start procedurestart time was before applying the gravity stimulation

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.50939
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.045986
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.423996
Spike_AFFX-r2-Bs-dap_5_signal12.315543
NoiseAvg:2.28,Std:0.06,Min:2.1,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.107639
#P13867
Spike_AFFX-r2-Bs-phe_M_signal15.766090
Corner-Avg:8062,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.480675
Spike_AFFX-r2-Ec-bioB_3_signal56.298695
Spike_AFFX-r2-Bs-lys_M_signal14.613750
Spike_AFFX-r2-P1-cre_3_signal3728.535156
Spike_AFFX-r2-Bs-lys_3-5-ratio1.779279
Spike_AFFX-r2-Bs-dap_M_signal65.042664
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.751572
Spike_AFFX-r2-Ec-bioB_avg-signal59.771694
Spike_AFFX-r2-Bs-thr_avg-signal36.860935
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal648.459106
Spike_AFFX-r2-Bs-phe_5_signal17.726957
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal946.454102
RawQ2.229387
Spike_AFFX-r2-Bs-lys_5_signal12.075282
Signal(A)2.885565
%A37.786060
Signal(All)147.335495
Corner+Avg:98,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal243.018112
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.659962
Spike_AFFX-r2-Ec-bioD_avg-signal797.456604
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.793510
Spike_AFFX-r2-Bs-lys_avg-signal16.058109
Spike_AFFX-r2-P1-cre_avg-signal3646.574463
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.420430
Spike_AFFX-r2-Bs-thr_3_signal77.881996
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.717669
Spike_AFFX-r2-Bs-dap_3_signal179.371506
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.459543
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal226.846863
#M324
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.485294
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.071287
Spike_AFFX-r2-Bs-thr_M_signal26.593182
Signal(P)240.284698
Spike_AFFX-r2-Bs-phe_3-5-ratio1.785978
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6301,Count:9
Spike_AFFX-r2-P1-cre_5_signal3564.613770
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8619
Signal(M)11.802156
BackgroundAvg:76.76,Std:0.46,Min:75.2,Max:77.9
Spike_AFFX-r2-Ec-bioC_avg-signal234.932495
Spike_AFFX-r2-Bs-dap_avg-signal85.576569
Spike_AFFX-r2-Bs-dap_3-5-ratio14.564644
Spike_AFFX-r2-Ec-bioB_5_signal39.535702
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.509390
NF1.000000
HZ4
Tau0.015000


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