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Experiment: Effect of compound 3 on somatic embryogenesis

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-596

The goal of this microarray experiment is to find the targets of compound 3 in Arabidopsis.on day 2,wildtype columbia seedlings were induced for 8 hours with compound 3.After 8 hours total RNA was isolated from whole seedlings including seedcoat.

About the Experimenter

Name:Mr Tom Stekelenburg
Head of Lab Name: Gerco Angenent
Lab:
Address:Business Unit Bioscience, Plant Research International B.V., Wageningen University
Post box nr 619, Wageningen, , 6700 AP, NETHERLANDS
Postcode:
Country:
 
Telephone Number: 0317-480889

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: compound_based_treatment
Number of Slides:6
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Stekelenburg: Effect of compound 3 on somatic embryogenesis

Slide: Stekelenburg_596-1_8hrs_DMSO_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 ("Stekelenburg_596-1_8hrs_DMSO_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: Stekelenburg_596-1_8hrs_DMSO_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 DMSO was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 DMSO was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
Other Information:

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:0.318493
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-ratio1.226574
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.968883
Spike_AFFX-r2-Bs-dap_5_signal8.809324
NoiseAvg:4.19,Std:0.09,Min:4.0,Max:4.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionM
Spike_AFFX-r2-Bs-thr_5_signal4.261308
#P14981
Spike_AFFX-r2-Bs-phe_M_signal8.793962
Corner-Avg:10570,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal9.522469
Spike_AFFX-r2-Ec-bioB_3_signal12.706131
Spike_AFFX-r2-Bs-lys_M_signal8.882623
Spike_AFFX-r2-P1-cre_3_signal3383.230713
Spike_AFFX-r2-Bs-lys_3-5-ratio0.673497
Spike_AFFX-r2-Bs-dap_M_signal23.854578
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.142023
Spike_AFFX-r2-Ec-bioB_avg-signal11.780936
Spike_AFFX-r2-Bs-thr_avg-signal12.748554
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal643.536743
Spike_AFFX-r2-Bs-phe_5_signal10.270168
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal885.081848
RawQ3.578684
Spike_AFFX-r2-Bs-lys_5_signal7.101750
Signal(A)3.234616
%A32.761948
Signal(All)142.955444
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal217.875015
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal10.254337
Spike_AFFX-r2-Ec-bioD_avg-signal764.309326
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.677338
Spike_AFFX-r2-Bs-lys_avg-signal6.922459
Spike_AFFX-r2-P1-cre_avg-signal3070.754395
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.560719
Spike_AFFX-r2-Bs-thr_3_signal21.911743
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-signal9.772822
Spike_AFFX-r2-Bs-dap_3_signal55.654434
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.375340
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.803223
#M356
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal4.783005
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.004944
Spike_AFFX-r2-Bs-thr_M_signal12.072613
Signal(P)215.760529
Spike_AFFX-r2-Bs-phe_3-5-ratio0.998459
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8183,Count:9
Spike_AFFX-r2-P1-cre_5_signal2758.277832
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7473
Signal(M)12.171206
BackgroundAvg:93.62,Std:1.03,Min:90.7,Max:96.6
Spike_AFFX-r2-Ec-bioC_avg-signal217.339111
Spike_AFFX-r2-Bs-dap_avg-signal29.439445
Spike_AFFX-r2-Bs-dap_3-5-ratio6.317674
Spike_AFFX-r2-Ec-bioB_5_signal13.114209
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.318493
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_596-2_8hrs_DMSO_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 ("Stekelenburg_596-2_8hrs_DMSO_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: Stekelenburg_596-2_8hrs_DMSO_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 DMSO was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 DMSO was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
Other Information:

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:0.387044
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-ratio1.152352
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.494846
Spike_AFFX-r2-Bs-dap_5_signal13.788460
NoiseAvg:4.64,Std:0.37,Min:4.1,Max:6.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal5.117988
#P14603
Spike_AFFX-r2-Bs-phe_M_signal6.749327
Corner-Avg:13710,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.915447
Spike_AFFX-r2-Ec-bioB_3_signal6.297903
Spike_AFFX-r2-Bs-lys_M_signal2.172270
Spike_AFFX-r2-P1-cre_3_signal2620.846680
Spike_AFFX-r2-Bs-lys_3-5-ratio1.335844
Spike_AFFX-r2-Bs-dap_M_signal27.899723
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.717251
Spike_AFFX-r2-Ec-bioB_avg-signal9.313449
Spike_AFFX-r2-Bs-thr_avg-signal10.662263
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal550.288879
Spike_AFFX-r2-Bs-phe_5_signal8.661366
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal809.234619
RawQ3.848601
Spike_AFFX-r2-Bs-lys_5_signal3.778673
Signal(A)3.888228
%A34.410347
Signal(All)141.440628
Corner+Avg:214,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.966782
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal3.582038
Spike_AFFX-r2-Ec-bioD_avg-signal679.761719
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.020164
Spike_AFFX-r2-Bs-lys_avg-signal3.666220
Spike_AFFX-r2-P1-cre_avg-signal2447.596436
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.569487
Spike_AFFX-r2-Bs-thr_3_signal13.906856
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-signal6.330910
Spike_AFFX-r2-Bs-dap_3_signal50.418736
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.470563
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal165.782227
#M358
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal5.047718
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.958889
Spike_AFFX-r2-Bs-thr_M_signal12.961946
Signal(P)218.507019
Spike_AFFX-r2-Bs-phe_3-5-ratio0.413565
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:13187,Count:9
Spike_AFFX-r2-P1-cre_5_signal2274.346191
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7849
Signal(M)13.642192
BackgroundAvg:100.12,Std:0.68,Min:98.3,Max:102.7
Spike_AFFX-r2-Ec-bioC_avg-signal162.374512
Spike_AFFX-r2-Bs-dap_avg-signal30.702307
Spike_AFFX-r2-Bs-dap_3-5-ratio3.656589
Spike_AFFX-r2-Ec-bioB_5_signal12.726997
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.387044
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_596-3_8hrs_DMSO_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 ("Stekelenburg_596-3_8hrs_DMSO_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: Stekelenburg_596-3_8hrs_DMSO_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 DMSO was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 DMSO was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
Other Information:

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:0.399611
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-ratio1.219974
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.652493
Spike_AFFX-r2-Bs-dap_5_signal12.084844
NoiseAvg:4.48,Std:0.12,Min:4.1,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal6.899066
#P14648
Spike_AFFX-r2-Bs-phe_M_signal5.785574
Corner-Avg:12980,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal4.129381
Spike_AFFX-r2-Ec-bioB_3_signal11.317860
Spike_AFFX-r2-Bs-lys_M_signal2.582085
Spike_AFFX-r2-P1-cre_3_signal2384.716553
Spike_AFFX-r2-Bs-lys_3-5-ratio1.122822
Spike_AFFX-r2-Bs-dap_M_signal22.693684
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.029291
Spike_AFFX-r2-Ec-bioB_avg-signal7.432068
Spike_AFFX-r2-Bs-thr_avg-signal13.801816
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal426.463074
Spike_AFFX-r2-Bs-phe_5_signal7.961788
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal634.746643
RawQ3.803463
Spike_AFFX-r2-Bs-lys_5_signal4.467739
Signal(A)3.825001
%A34.090313
Signal(All)140.649750
Corner+Avg:221,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal138.174545
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal10.374174
Spike_AFFX-r2-Ec-bioD_avg-signal530.604858
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.217445
Spike_AFFX-r2-Bs-lys_avg-signal4.022099
Spike_AFFX-r2-P1-cre_avg-signal2169.722168
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.692240
Spike_AFFX-r2-Bs-thr_3_signal20.899282
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-signal8.040512
Spike_AFFX-r2-Bs-dap_3_signal35.942970
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.488398
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal130.841614
#M386
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal5.016474
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.056044
Spike_AFFX-r2-Bs-thr_M_signal13.607100
Signal(P)216.618484
Spike_AFFX-r2-Bs-phe_3-5-ratio1.302996
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:12147,Count:9
Spike_AFFX-r2-P1-cre_5_signal1954.727783
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7776
Signal(M)14.119245
BackgroundAvg:99.98,Std:1.83,Min:96.0,Max:104.7
Spike_AFFX-r2-Ec-bioC_avg-signal134.508087
Spike_AFFX-r2-Bs-dap_avg-signal23.573832
Spike_AFFX-r2-Bs-dap_3-5-ratio2.974219
Spike_AFFX-r2-Ec-bioB_5_signal6.848963
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.399611
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_596-4_8hrs_Compound-3_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 ("Stekelenburg_596-4_8hrs_Compound-3_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: Stekelenburg_596-4_8hrs_Compound-3_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 Compound 3 was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 25µM Compound 3 was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
Other Information:

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:0.440266
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-ratio1.199620
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.143746
Spike_AFFX-r2-Bs-dap_5_signal22.529076
NoiseAvg:3.91,Std:0.12,Min:3.5,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.869716
#P14889
Spike_AFFX-r2-Bs-phe_M_signal9.473890
Corner-Avg:13594,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.634985
Spike_AFFX-r2-Ec-bioB_3_signal11.954232
Spike_AFFX-r2-Bs-lys_M_signal6.704624
Spike_AFFX-r2-P1-cre_3_signal3082.651611
Spike_AFFX-r2-Bs-lys_3-5-ratio1.125164
Spike_AFFX-r2-Bs-dap_M_signal41.038921
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.717458
Spike_AFFX-r2-Ec-bioB_avg-signal10.347013
Spike_AFFX-r2-Bs-thr_avg-signal13.783050
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal653.813538
Spike_AFFX-r2-Bs-phe_5_signal8.879199
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal877.078186
RawQ3.508817
Spike_AFFX-r2-Bs-lys_5_signal5.710422
Signal(A)3.399849
%A33.213501
Signal(All)142.301132
Corner+Avg:218,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal169.931396
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal12.306151
Spike_AFFX-r2-Ec-bioD_avg-signal765.445862
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P65.274002
Spike_AFFX-r2-Bs-lys_avg-signal6.280069
Spike_AFFX-r2-P1-cre_avg-signal2826.170410
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal21.385626
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-signal10.219747
Spike_AFFX-r2-Bs-dap_3_signal55.799664
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.341481
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal178.609528
#M345
Spike_AFFX-r2-Bs-lys_5_detectionM
Spike_AFFX-r2-Bs-lys_3_signal6.425160
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.951413
Spike_AFFX-r2-Bs-thr_M_signal12.093803
Signal(P)215.967560
Spike_AFFX-r2-Bs-phe_3-5-ratio1.385953
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10036,Count:9
Spike_AFFX-r2-P1-cre_5_signal2569.689209
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7576
Signal(M)13.305991
BackgroundAvg:91.55,Std:0.86,Min:89.6,Max:94.1
Spike_AFFX-r2-Ec-bioC_avg-signal174.270462
Spike_AFFX-r2-Bs-dap_avg-signal39.789219
Spike_AFFX-r2-Bs-dap_3-5-ratio2.476784
Spike_AFFX-r2-Ec-bioB_5_signal10.451822
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.440266
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_596-5_8hrs_Compound-3_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 ("Stekelenburg_596-5_8hrs_Compound-3_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: Stekelenburg_596-5_8hrs_Compound-3_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 Compound 3 was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 25µM Compound 3 was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
Other Information:

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:0.446972
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-ratio1.538888
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.076265
Spike_AFFX-r2-Bs-dap_5_signal24.452074
NoiseAvg:3.61,Std:0.10,Min:3.3,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal8.973586
#P14962
Spike_AFFX-r2-Bs-phe_M_signal6.980516
Corner-Avg:12969,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.410285
Spike_AFFX-r2-Ec-bioB_3_signal9.848701
Spike_AFFX-r2-Bs-lys_M_signal7.659286
Spike_AFFX-r2-P1-cre_3_signal3061.911377
Spike_AFFX-r2-Bs-lys_3-5-ratio0.313827
Spike_AFFX-r2-Bs-dap_M_signal31.177366
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.232419
Spike_AFFX-r2-Ec-bioB_avg-signal9.803267
Spike_AFFX-r2-Bs-thr_avg-signal13.795560
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal594.082642
Spike_AFFX-r2-Bs-phe_5_signal7.290141
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal882.694763
RawQ3.228901
Spike_AFFX-r2-Bs-lys_5_signal6.660860
Signal(A)3.352745
%A32.902237
Signal(All)141.362930
Corner+Avg:198,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.072220
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal7.055283
Spike_AFFX-r2-Ec-bioD_avg-signal738.388672
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.594040
Spike_AFFX-r2-Bs-lys_avg-signal5.470167
Spike_AFFX-r2-P1-cre_avg-signal2525.801270
Spike_AFFX-r2-Ec-bioB_M_detectionM
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.503726
Spike_AFFX-r2-Bs-thr_3_signal20.032804
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-signal7.108646
Spike_AFFX-r2-Bs-dap_3_signal55.606075
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.485811
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal192.008362
#M343
Spike_AFFX-r2-Bs-lys_5_detectionM
Spike_AFFX-r2-Bs-lys_3_signal2.090356
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.823257
Spike_AFFX-r2-Bs-thr_M_signal12.380287
Signal(P)213.537216
Spike_AFFX-r2-Bs-phe_3-5-ratio0.967784
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11543,Count:9
Spike_AFFX-r2-P1-cre_5_signal1989.690918
Spike_AFFX-r2-Bs-phe_M_detectionM
#A7505
Signal(M)12.776608
BackgroundAvg:80.27,Std:0.53,Min:78.7,Max:81.9
Spike_AFFX-r2-Ec-bioC_avg-signal175.040283
Spike_AFFX-r2-Bs-dap_avg-signal37.078503
Spike_AFFX-r2-Bs-dap_3-5-ratio2.274084
Spike_AFFX-r2-Ec-bioB_5_signal9.150814
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.446972
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_596-6_8hrs_Compound-3_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 ("Stekelenburg_596-6_8hrs_Compound-3_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: Stekelenburg_596-6_8hrs_Compound-3_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 Compound 3 was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 25µM Compound 3 was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
Other Information:

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:0.378327
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-ratio1.293796
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.255661
Spike_AFFX-r2-Bs-dap_5_signal22.304375
NoiseAvg:3.35,Std:0.07,Min:3.1,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.893667
#P15199
Spike_AFFX-r2-Bs-phe_M_signal5.620766
Corner-Avg:8488,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.002608
Spike_AFFX-r2-Ec-bioB_3_signal13.145251
Spike_AFFX-r2-Bs-lys_M_signal5.611062
Spike_AFFX-r2-P1-cre_3_signal3376.273682
Spike_AFFX-r2-Bs-lys_3-5-ratio0.762023
Spike_AFFX-r2-Bs-dap_M_signal31.374029
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.670522
Spike_AFFX-r2-Ec-bioB_avg-signal11.205548
Spike_AFFX-r2-Bs-thr_avg-signal16.230206
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal607.803955
Spike_AFFX-r2-Bs-phe_5_signal9.790504
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal836.401428
RawQ3.104059
Spike_AFFX-r2-Bs-lys_5_signal4.829899
Signal(A)2.640805
%A31.994740
Signal(All)141.663284
Corner+Avg:140,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal235.629272
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal7.729071
Spike_AFFX-r2-Ec-bioD_avg-signal722.102661
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.633057
Spike_AFFX-r2-Bs-lys_avg-signal4.707151
Spike_AFFX-r2-P1-cre_avg-signal2992.930176
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.372205
Spike_AFFX-r2-Bs-thr_3_signal25.303356
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-signal7.713448
Spike_AFFX-r2-Bs-dap_3_signal58.963573
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.376104
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal226.241714
#M313
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal3.680492
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.041494
Spike_AFFX-r2-Bs-thr_M_signal16.493597
Signal(P)211.118225
Spike_AFFX-r2-Bs-phe_3-5-ratio0.789446
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6572,Count:9
Spike_AFFX-r2-P1-cre_5_signal2609.586426
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7298
Signal(M)10.482686
BackgroundAvg:80.69,Std:0.82,Min:77.8,Max:83.0
Spike_AFFX-r2-Ec-bioC_avg-signal230.935486
Spike_AFFX-r2-Bs-dap_avg-signal37.547325
Spike_AFFX-r2-Bs-dap_3-5-ratio2.643588
Spike_AFFX-r2-Ec-bioB_5_signal10.468787
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.378327
NF1.000000
HZ4
Tau0.015000


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