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Experiment: Characterization of FBK mutant and OX lines

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-624

Characterization of transcriptional profiles of four F-box gene mutants/overexpressors (AT1G15670, AT1G80440, AT2G44130, AT3G59940; see also Schumann et al., Plant Physiol 155:835). Samples have been prepared from 9d-old seedlings and open flowers (stage 15, 45d-old).

About the Experimenter

Name: Marcel Quint
Head of Lab Name: Marcel Quint
Lab:
Address:Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry
Weinberg 3 , Halle, Sachsen-Anhalt, 06120, GERMANY
Postcode: 06120
Country: GERMANY
 
Telephone Number: +49-345-55821480
Fax Number: +49-345-5582-1409

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
Number of Slides:36
 
Experimental Parameters:
parametergenetic_modification
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Quint: Characterization of FBK mutant and OX lines

Slide: Quint_624-1_35S::AT1G15670_9-day_seedlings_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 ("Quint_624-1_35S::AT1G15670_9-day_seedlings_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: Quint_624-1_35S::AT1G15670_9-day_seedlings_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G15670
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclavation
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G15670
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.473909
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-ratio1.301278
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.008660
Spike_AFFX-r2-Bs-dap_5_signal49.544685
NoiseAvg:3.11,Std:0.07,Min:2.9,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_signal13.477155
#P15427
Spike_AFFX-r2-Bs-phe_M_signal28.091080
Corner-Avg:13812,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal24.854856
Spike_AFFX-r2-Ec-bioB_3_signal21.127314
Spike_AFFX-r2-Bs-lys_M_signal16.955517
Spike_AFFX-r2-P1-cre_3_signal3962.220215
Spike_AFFX-r2-Bs-lys_3-5-ratio2.593480
Spike_AFFX-r2-Bs-dap_M_signal159.890381
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.614682
Spike_AFFX-r2-Ec-bioB_avg-signal22.309362
Spike_AFFX-r2-Bs-thr_avg-signal48.538509
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal756.050659
Spike_AFFX-r2-Bs-phe_5_signal17.478373
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1104.314697
RawQ2.609552
Spike_AFFX-r2-Bs-lys_5_signal12.752021
Signal(A)4.639662
%A30.363876
Signal(All)139.207672
Corner+Avg:230,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal232.790070
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal47.430668
Spike_AFFX-r2-Ec-bioD_avg-signal930.182678
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.632614
Spike_AFFX-r2-Bs-lys_avg-signal20.926550
Spike_AFFX-r2-P1-cre_avg-signal3503.543945
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.003507
Spike_AFFX-r2-Bs-thr_3_signal89.147095
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-signal31.000038
Spike_AFFX-r2-Bs-dap_3_signal318.400208
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.460636
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal226.772095
#M457
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.072113
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.026538
Spike_AFFX-r2-Bs-thr_M_signal42.991268
Signal(P)203.273682
Spike_AFFX-r2-Bs-phe_3-5-ratio2.713678
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11914,Count:9
Spike_AFFX-r2-P1-cre_5_signal3044.867676
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6926
Signal(M)15.950971
BackgroundAvg:59.83,Std:0.57,Min:58.3,Max:61.3
Spike_AFFX-r2-Ec-bioC_avg-signal229.781082
Spike_AFFX-r2-Bs-dap_avg-signal175.945084
Spike_AFFX-r2-Bs-dap_3-5-ratio6.426526
Spike_AFFX-r2-Ec-bioB_5_signal20.945919
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.473909
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-2_35S::AT1G15670_9-day_seedlings_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 ("Quint_624-2_35S::AT1G15670_9-day_seedlings_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: Quint_624-2_35S::AT1G15670_9-day_seedlings_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G15670
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G15670
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.596964
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-ratio0.986433
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.184567
Spike_AFFX-r2-Bs-dap_5_signal36.952358
NoiseAvg:3.11,Std:0.14,Min:2.8,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_signal12.268173
#P14973
Spike_AFFX-r2-Bs-phe_M_signal30.663023
Corner-Avg:11993,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal21.246496
Spike_AFFX-r2-Ec-bioB_3_signal22.331703
Spike_AFFX-r2-Bs-lys_M_signal11.920192
Spike_AFFX-r2-P1-cre_3_signal3046.078369
Spike_AFFX-r2-Bs-lys_3-5-ratio2.949016
Spike_AFFX-r2-Bs-dap_M_signal165.645203
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.563795
Spike_AFFX-r2-Ec-bioB_avg-signal20.810135
Spike_AFFX-r2-Bs-thr_avg-signal59.387676
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal685.599548
Spike_AFFX-r2-Bs-phe_5_signal19.448812
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1093.251465
RawQ2.695959
Spike_AFFX-r2-Bs-lys_5_signal16.166906
Signal(A)5.204988
%A32.634808
Signal(All)141.311691
Corner+Avg:211,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal211.313400
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.201271
Spike_AFFX-r2-Ec-bioD_avg-signal889.425537
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.642265
Spike_AFFX-r2-Bs-lys_avg-signal25.254522
Spike_AFFX-r2-P1-cre_avg-signal3067.025391
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal117.330292
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-signal37.104370
Spike_AFFX-r2-Bs-dap_3_signal294.166779
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.594592
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal214.720978
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.676468
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.984130
Spike_AFFX-r2-Bs-thr_M_signal48.564560
Signal(P)212.256149
Spike_AFFX-r2-Bs-phe_3-5-ratio3.146787
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11018,Count:9
Spike_AFFX-r2-P1-cre_5_signal3087.972168
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7444
Signal(M)16.443651
BackgroundAvg:63.39,Std:0.64,Min:62.0,Max:65.1
Spike_AFFX-r2-Ec-bioC_avg-signal213.017181
Spike_AFFX-r2-Bs-dap_avg-signal165.588120
Spike_AFFX-r2-Bs-dap_3-5-ratio7.960704
Spike_AFFX-r2-Ec-bioB_5_signal18.852201
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.596964
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-3_35S::AT1G15670_9-day_seedlings_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 ("Quint_624-3_35S::AT1G15670_9-day_seedlings_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: Quint_624-3_35S::AT1G15670_9-day_seedlings_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G15670
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G15670
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.401009
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-ratio1.182491
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.928239
Spike_AFFX-r2-Bs-dap_5_signal47.765762
NoiseAvg:3.26,Std:0.07,Min:3.0,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_signal15.941557
#P15490
Spike_AFFX-r2-Bs-phe_M_signal30.855925
Corner-Avg:15371,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal20.131651
Spike_AFFX-r2-Ec-bioB_3_signal19.268637
Spike_AFFX-r2-Bs-lys_M_signal12.998475
Spike_AFFX-r2-P1-cre_3_signal3054.113281
Spike_AFFX-r2-Bs-lys_3-5-ratio3.671474
Spike_AFFX-r2-Bs-dap_M_signal187.490570
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.564530
Spike_AFFX-r2-Ec-bioB_avg-signal20.052855
Spike_AFFX-r2-Bs-thr_avg-signal48.042999
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal571.013428
Spike_AFFX-r2-Bs-phe_5_signal18.338186
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal915.550049
RawQ2.591942
Spike_AFFX-r2-Bs-lys_5_signal13.865000
Signal(A)4.246849
%A30.385796
Signal(All)137.833160
Corner+Avg:304,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal192.749527
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal70.003784
Spike_AFFX-r2-Ec-bioD_avg-signal743.281738
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.908813
Spike_AFFX-r2-Bs-lys_avg-signal25.922821
Spike_AFFX-r2-P1-cre_avg-signal2818.446533
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_signal88.707268
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-signal39.732632
Spike_AFFX-r2-Bs-dap_3_signal318.194763
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.603377
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal187.565811
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.904991
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.027637
Spike_AFFX-r2-Bs-thr_M_signal39.480175
Signal(P)200.692276
Spike_AFFX-r2-Bs-phe_3-5-ratio3.817378
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13460,Count:9
Spike_AFFX-r2-P1-cre_5_signal2582.779785
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6931
Signal(M)14.952008
BackgroundAvg:62.75,Std:0.52,Min:60.7,Max:64.1
Spike_AFFX-r2-Ec-bioC_avg-signal190.157669
Spike_AFFX-r2-Bs-dap_avg-signal184.483704
Spike_AFFX-r2-Bs-dap_3-5-ratio6.661566
Spike_AFFX-r2-Ec-bioB_5_signal20.758278
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.401009
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-4_35S::AT2G44130_9-day_seedlings_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 ("Quint_624-4_35S::AT2G44130_9-day_seedlings_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: Quint_624-4_35S::AT2G44130_9-day_seedlings_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT2G44130
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT2G44130
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.606773
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-ratio1.008718
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.516050
Spike_AFFX-r2-Bs-dap_5_signal27.902416
NoiseAvg:3.14,Std:0.10,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_signal14.632054
#P14886
Spike_AFFX-r2-Bs-phe_M_signal29.381813
Corner-Avg:13907,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal24.393867
Spike_AFFX-r2-Ec-bioB_3_signal15.723112
Spike_AFFX-r2-Bs-lys_M_signal13.630724
Spike_AFFX-r2-P1-cre_3_signal3380.321533
Spike_AFFX-r2-Bs-lys_3-5-ratio3.215325
Spike_AFFX-r2-Bs-dap_M_signal122.945900
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.206076
Spike_AFFX-r2-Ec-bioB_avg-signal23.528391
Spike_AFFX-r2-Bs-thr_avg-signal42.352757
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal874.807556
Spike_AFFX-r2-Bs-phe_5_signal13.906689
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1144.778564
RawQ2.787418
Spike_AFFX-r2-Bs-lys_5_signal10.856688
Signal(A)5.276585
%A32.897850
Signal(All)142.072952
Corner+Avg:242,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal218.496552
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal40.304409
Spike_AFFX-r2-Ec-bioD_avg-signal1009.793091
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.260849
Spike_AFFX-r2-Bs-lys_avg-signal19.798399
Spike_AFFX-r2-P1-cre_avg-signal3365.714355
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_signal76.175591
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-signal27.864304
Spike_AFFX-r2-Bs-dap_3_signal227.178268
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.308606
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal217.361374
#M420
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.907784
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.005223
Spike_AFFX-r2-Bs-thr_M_signal36.250614
Signal(P)214.519592
Spike_AFFX-r2-Bs-phe_3-5-ratio2.898203
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11047,Count:9
Spike_AFFX-r2-P1-cre_5_signal3351.106934
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7504
Signal(M)18.451876
BackgroundAvg:67.90,Std:0.68,Min:65.7,Max:69.3
Spike_AFFX-r2-Ec-bioC_avg-signal217.928955
Spike_AFFX-r2-Bs-dap_avg-signal126.008858
Spike_AFFX-r2-Bs-dap_3-5-ratio8.141885
Spike_AFFX-r2-Ec-bioB_5_signal30.468195
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.606773
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-5_35S::AT2G44130_9-day_seedlings_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 ("Quint_624-5_35S::AT2G44130_9-day_seedlings_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: Quint_624-5_35S::AT2G44130_9-day_seedlings_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT2G44130
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT2G44130
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.448013
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-ratio1.197977
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.067306
Spike_AFFX-r2-Bs-dap_5_signal47.016640
NoiseAvg:3.19,Std:0.09,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_signal18.302675
#P15430
Spike_AFFX-r2-Bs-phe_M_signal32.892727
Corner-Avg:14297,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal22.797861
Spike_AFFX-r2-Ec-bioB_3_signal23.514273
Spike_AFFX-r2-Bs-lys_M_signal13.912403
Spike_AFFX-r2-P1-cre_3_signal3610.029053
Spike_AFFX-r2-Bs-lys_3-5-ratio2.923939
Spike_AFFX-r2-Bs-dap_M_signal158.487228
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.957208
Spike_AFFX-r2-Ec-bioB_avg-signal22.781187
Spike_AFFX-r2-Bs-thr_avg-signal43.087170
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal686.735046
Spike_AFFX-r2-Bs-phe_5_signal24.412451
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1166.525879
RawQ2.606169
Spike_AFFX-r2-Bs-lys_5_signal12.271996
Signal(A)4.414689
%A30.657606
Signal(All)139.365982
Corner+Avg:241,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal215.419098
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal53.967728
Spike_AFFX-r2-Ec-bioD_avg-signal926.630493
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.645767
Spike_AFFX-r2-Bs-lys_avg-signal20.688990
Spike_AFFX-r2-P1-cre_avg-signal3311.733398
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_signal72.427490
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-signal37.090969
Spike_AFFX-r2-Bs-dap_3_signal299.399353
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.698655
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal215.393463
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.882568
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.000119
Spike_AFFX-r2-Bs-thr_M_signal38.531342
Signal(P)203.644958
Spike_AFFX-r2-Bs-phe_3-5-ratio2.210664
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12764,Count:9
Spike_AFFX-r2-P1-cre_5_signal3013.437988
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6993
Signal(M)15.050032
BackgroundAvg:63.58,Std:0.31,Min:62.7,Max:64.4
Spike_AFFX-r2-Ec-bioC_avg-signal215.406281
Spike_AFFX-r2-Bs-dap_avg-signal168.301071
Spike_AFFX-r2-Bs-dap_3-5-ratio6.367945
Spike_AFFX-r2-Ec-bioB_5_signal22.031427
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.448013
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-6_35S::AT2G44130_9-day_seedlings_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 ("Quint_624-6_35S::AT2G44130_9-day_seedlings_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: Quint_624-6_35S::AT2G44130_9-day_seedlings_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT2G44130
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT2G44130
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.49212
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-ratio1.189790
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.694923
Spike_AFFX-r2-Bs-dap_5_signal57.054806
NoiseAvg:3.32,Std:0.09,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_signal17.492815
#P15178
Spike_AFFX-r2-Bs-phe_M_signal34.626476
Corner-Avg:14446,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal23.017801
Spike_AFFX-r2-Ec-bioB_3_signal22.641830
Spike_AFFX-r2-Bs-lys_M_signal19.793348
Spike_AFFX-r2-P1-cre_3_signal3798.036865
Spike_AFFX-r2-Bs-lys_3-5-ratio2.605756
Spike_AFFX-r2-Bs-dap_M_signal195.367371
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.361481
Spike_AFFX-r2-Ec-bioB_avg-signal26.080475
Spike_AFFX-r2-Bs-thr_avg-signal60.355118
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal713.126526
Spike_AFFX-r2-Bs-phe_5_signal22.607746
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1158.063232
RawQ2.714097
Spike_AFFX-r2-Bs-lys_5_signal24.240170
Signal(A)4.904175
%A31.648399
Signal(All)140.743088
Corner+Avg:250,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal253.399323
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal55.927193
Spike_AFFX-r2-Ec-bioD_avg-signal935.594849
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.540993
Spike_AFFX-r2-Bs-lys_avg-signal35.732494
Spike_AFFX-r2-P1-cre_avg-signal3495.114258
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.810609
Spike_AFFX-r2-Bs-thr_3_signal111.280205
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-signal37.720470
Spike_AFFX-r2-Bs-dap_3_signal346.815125
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.623924
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.195114
#M413
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal63.163967
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.033460
Spike_AFFX-r2-Bs-thr_M_signal52.292328
Signal(P)208.736572
Spike_AFFX-r2-Bs-phe_3-5-ratio2.473807
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13122,Count:9
Spike_AFFX-r2-P1-cre_5_signal3192.191895
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7219
Signal(M)16.326757
BackgroundAvg:67.19,Std:0.57,Min:65.7,Max:68.7
Spike_AFFX-r2-Ec-bioC_avg-signal249.297211
Spike_AFFX-r2-Bs-dap_avg-signal199.745773
Spike_AFFX-r2-Bs-dap_3-5-ratio6.078631
Spike_AFFX-r2-Ec-bioB_5_signal32.581795
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.492120
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-7_35S::AT1G80440_9-day_seedlings_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 ("Quint_624-7_35S::AT1G80440_9-day_seedlings_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: Quint_624-7_35S::AT1G80440_9-day_seedlings_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G80440
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G80440
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.992086
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-ratio1.309855
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.633062
Spike_AFFX-r2-Bs-dap_5_signal112.828583
NoiseAvg:2.78,Std:0.09,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_signal23.044901
#P13829
Spike_AFFX-r2-Bs-phe_M_signal57.901421
Corner-Avg:13248,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal49.037258
Spike_AFFX-r2-Ec-bioB_3_signal31.439520
Spike_AFFX-r2-Bs-lys_M_signal72.511917
Spike_AFFX-r2-P1-cre_3_signal6570.243652
Spike_AFFX-r2-Bs-lys_3-5-ratio2.594787
Spike_AFFX-r2-Bs-dap_M_signal410.303223
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio16.840790
Spike_AFFX-r2-Ec-bioB_avg-signal43.379810
Spike_AFFX-r2-Bs-thr_avg-signal175.953598
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1301.213501
Spike_AFFX-r2-Bs-phe_5_signal82.713272
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2686.200928
RawQ2.607590
Spike_AFFX-r2-Bs-lys_5_signal42.943726
Signal(A)7.397821
%A37.032005
Signal(All)151.209869
Corner+Avg:222,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal401.346741
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal141.797272
Spike_AFFX-r2-Ec-bioD_avg-signal1993.707275
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.626919
Spike_AFFX-r2-Bs-lys_avg-signal75.628487
Spike_AFFX-r2-P1-cre_avg-signal5793.125977
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.341079
Spike_AFFX-r2-Bs-thr_3_signal388.094330
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-signal94.137329
Spike_AFFX-r2-Bs-dap_3_signal848.509155
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.064381
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal494.021790
#M534
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal111.429817
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.812407
Spike_AFFX-r2-Bs-thr_M_signal116.721542
Signal(P)243.868286
Spike_AFFX-r2-Bs-phe_3-5-ratio1.714323
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11805,Count:9
Spike_AFFX-r2-P1-cre_5_signal5016.008301
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8447
Signal(M)26.504150
BackgroundAvg:61.47,Std:0.41,Min:60.5,Max:62.5
Spike_AFFX-r2-Ec-bioC_avg-signal447.684265
Spike_AFFX-r2-Bs-dap_avg-signal457.213654
Spike_AFFX-r2-Bs-dap_3-5-ratio7.520339
Spike_AFFX-r2-Ec-bioB_5_signal49.662651
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.992086
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-8_35S::AT1G80440_9-day_seedlings_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 ("Quint_624-8_35S::AT1G80440_9-day_seedlings_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: Quint_624-8_35S::AT1G80440_9-day_seedlings_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G80440
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G80440
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.53352
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-ratio1.380144
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.726765
Spike_AFFX-r2-Bs-dap_5_signal41.805325
NoiseAvg:3.72,Std:0.09,Min:3.5,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.092464
#P14552
Spike_AFFX-r2-Bs-phe_M_signal30.924171
Corner-Avg:13292,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal32.540287
Spike_AFFX-r2-Ec-bioB_3_signal18.792006
Spike_AFFX-r2-Bs-lys_M_signal16.948654
Spike_AFFX-r2-P1-cre_3_signal5029.242188
Spike_AFFX-r2-Bs-lys_3-5-ratio2.447016
Spike_AFFX-r2-Bs-dap_M_signal143.910049
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.150670
Spike_AFFX-r2-Ec-bioB_avg-signal25.729780
Spike_AFFX-r2-Bs-thr_avg-signal41.237263
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1012.499451
Spike_AFFX-r2-Bs-phe_5_signal14.028630
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1688.323242
RawQ3.088844
Spike_AFFX-r2-Bs-lys_5_signal14.413949
Signal(A)5.842970
%A33.958790
Signal(All)145.570404
Corner+Avg:240,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal293.793335
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal54.257534
Spike_AFFX-r2-Ec-bioD_avg-signal1350.411377
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.796581
Spike_AFFX-r2-Bs-lys_avg-signal22.211258
Spike_AFFX-r2-P1-cre_avg-signal4336.620117
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.244630
Spike_AFFX-r2-Bs-thr_3_signal79.318550
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-signal33.070110
Spike_AFFX-r2-Bs-dap_3_signal346.050385
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.667481
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal346.049011
#M512
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.271172
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.848993
Spike_AFFX-r2-Bs-thr_M_signal33.300770
Signal(P)224.309814
Spike_AFFX-r2-Bs-phe_3-5-ratio3.867629
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12226,Count:9
Spike_AFFX-r2-P1-cre_5_signal3643.998047
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7746
Signal(M)21.571741
BackgroundAvg:76.67,Std:0.52,Min:75.4,Max:78.2
Spike_AFFX-r2-Ec-bioC_avg-signal319.921173
Spike_AFFX-r2-Bs-dap_avg-signal177.255249
Spike_AFFX-r2-Bs-dap_3-5-ratio8.277663
Spike_AFFX-r2-Ec-bioB_5_signal25.857048
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.533520
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-9_35S::AT1G80440_9-day_seedlings_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 ("Quint_624-9_35S::AT1G80440_9-day_seedlings_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: Quint_624-9_35S::AT1G80440_9-day_seedlings_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G80440
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G80440
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.813162
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-ratio1.389572
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.854335
Spike_AFFX-r2-Bs-dap_5_signal35.000599
NoiseAvg:2.96,Std:0.11,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_signal12.139227
#P14100
Spike_AFFX-r2-Bs-phe_M_signal26.132275
Corner-Avg:12594,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal36.662743
Spike_AFFX-r2-Ec-bioB_3_signal24.427519
Spike_AFFX-r2-Bs-lys_M_signal15.384234
Spike_AFFX-r2-P1-cre_3_signal6400.562012
Spike_AFFX-r2-Bs-lys_3-5-ratio4.114595
Spike_AFFX-r2-Bs-dap_M_signal157.222427
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.573489
Spike_AFFX-r2-Ec-bioB_avg-signal29.894232
Spike_AFFX-r2-Bs-thr_avg-signal59.973446
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1287.395142
Spike_AFFX-r2-Bs-phe_5_signal23.004158
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2044.680420
RawQ2.593656
Spike_AFFX-r2-Bs-lys_5_signal15.229109
Signal(A)6.845450
%A36.137657
Signal(All)148.874557
Corner+Avg:217,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal311.103516
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal49.338543
Spike_AFFX-r2-Ec-bioD_avg-signal1666.037842
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.814995
Spike_AFFX-r2-Bs-lys_avg-signal31.091652
Spike_AFFX-r2-P1-cre_avg-signal5503.350098
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.047348
Spike_AFFX-r2-Bs-thr_3_signal116.214760
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-signal32.824993
Spike_AFFX-r2-Bs-dap_3_signal378.267975
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.588231
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal424.804626
#M467
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal62.661613
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.732345
Spike_AFFX-r2-Bs-thr_M_signal51.566357
Signal(P)236.052200
Spike_AFFX-r2-Bs-phe_3-5-ratio2.144766
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9905,Count:9
Spike_AFFX-r2-P1-cre_5_signal4606.138184
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8243
Signal(M)23.695278
BackgroundAvg:62.12,Std:0.52,Min:61.3,Max:63.6
Spike_AFFX-r2-Ec-bioC_avg-signal367.954071
Spike_AFFX-r2-Bs-dap_avg-signal190.163681
Spike_AFFX-r2-Bs-dap_3-5-ratio10.807471
Spike_AFFX-r2-Ec-bioB_5_signal28.592434
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.813162
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-10_35S::AT3G59940_9-day_seedlings_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 ("Quint_624-10_35S::AT3G59940_9-day_seedlings_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: Quint_624-10_35S::AT3G59940_9-day_seedlings_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT3G59940
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT3G59940
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.333937
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-ratio1.244814
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.133152
Spike_AFFX-r2-Bs-dap_5_signal41.929111
NoiseAvg:3.43,Std:0.08,Min:3.1,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_signal14.880805
#P15734
Spike_AFFX-r2-Bs-phe_M_signal27.125277
Corner-Avg:14808,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal18.877068
Spike_AFFX-r2-Ec-bioB_3_signal15.851974
Spike_AFFX-r2-Bs-lys_M_signal11.469745
Spike_AFFX-r2-P1-cre_3_signal3077.652832
Spike_AFFX-r2-Bs-lys_3-5-ratio1.738009
Spike_AFFX-r2-Bs-dap_M_signal170.178680
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.173547
Spike_AFFX-r2-Ec-bioB_avg-signal16.239439
Spike_AFFX-r2-Bs-thr_avg-signal49.277607
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal591.978821
Spike_AFFX-r2-Bs-phe_5_signal17.824392
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal946.733643
RawQ2.856291
Spike_AFFX-r2-Bs-lys_5_signal18.967339
Signal(A)3.209625
%A29.447611
Signal(All)136.989685
Corner+Avg:261,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal167.428833
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal63.089119
Spike_AFFX-r2-Ec-bioD_avg-signal769.356201
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.978516
Spike_AFFX-r2-Bs-lys_avg-signal21.134161
Spike_AFFX-r2-P1-cre_avg-signal2775.016113
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_signal91.867348
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-signal36.012928
Spike_AFFX-r2-Bs-dap_3_signal337.380585
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.599269
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal178.996811
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.965401
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.935373
Spike_AFFX-r2-Bs-thr_M_signal41.084679
Signal(P)196.938980
Spike_AFFX-r2-Bs-phe_3-5-ratio3.539482
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12321,Count:9
Spike_AFFX-r2-P1-cre_5_signal2472.379395
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6717
Signal(M)12.639915
BackgroundAvg:70.74,Std:0.64,Min:69.4,Max:72.4
Spike_AFFX-r2-Ec-bioC_avg-signal173.212830
Spike_AFFX-r2-Bs-dap_avg-signal183.162796
Spike_AFFX-r2-Bs-dap_3-5-ratio8.046452
Spike_AFFX-r2-Ec-bioB_5_signal13.989275
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.333937
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-11_35S::AT3G59940_9-day_seedlings_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 ("Quint_624-11_35S::AT3G59940_9-day_seedlings_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: Quint_624-11_35S::AT3G59940_9-day_seedlings_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT3G59940
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT3G59940
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.554952
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-ratio1.330614
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.392975
Spike_AFFX-r2-Bs-dap_5_signal59.824074
NoiseAvg:2.73,Std:0.09,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.379503
#P15124
Spike_AFFX-r2-Bs-phe_M_signal47.321693
Corner-Avg:8053,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.831929
Spike_AFFX-r2-Ec-bioB_3_signal11.575981
Spike_AFFX-r2-Bs-lys_M_signal16.273281
Spike_AFFX-r2-P1-cre_3_signal4696.623535
Spike_AFFX-r2-Bs-lys_3-5-ratio2.203717
Spike_AFFX-r2-Bs-dap_M_signal290.994171
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.672299
Spike_AFFX-r2-Ec-bioB_avg-signal10.239388
Spike_AFFX-r2-Bs-thr_avg-signal83.551262
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal819.577393
Spike_AFFX-r2-Bs-phe_5_signal40.146545
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1094.569702
RawQ2.366150
Spike_AFFX-r2-Bs-lys_5_signal28.756218
Signal(A)4.701315
%A31.823761
Signal(All)144.102066
Corner+Avg:144,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal233.963348
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal95.994545
Spike_AFFX-r2-Ec-bioD_avg-signal957.073547
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.304253
Spike_AFFX-r2-Bs-lys_avg-signal36.133358
Spike_AFFX-r2-P1-cre_avg-signal4113.145020
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.871986
Spike_AFFX-r2-Bs-thr_3_signal179.514160
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-signal61.154263
Spike_AFFX-r2-Bs-dap_3_signal482.866730
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.335529
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal233.691483
#M427
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal63.370579
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.001163
Spike_AFFX-r2-Bs-thr_M_signal55.760124
Signal(P)214.612579
Spike_AFFX-r2-Bs-phe_3-5-ratio2.391104
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6073,Count:9
Spike_AFFX-r2-P1-cre_5_signal3529.666260
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7259
Signal(M)16.488430
BackgroundAvg:54.81,Std:0.35,Min:53.7,Max:56.1
Spike_AFFX-r2-Ec-bioC_avg-signal233.827423
Spike_AFFX-r2-Bs-dap_avg-signal277.894989
Spike_AFFX-r2-Bs-dap_3-5-ratio8.071445
Spike_AFFX-r2-Ec-bioB_5_signal8.310256
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.554952
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-12_35S::AT3G59940_9-day_seedlings_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 ("Quint_624-12_35S::AT3G59940_9-day_seedlings_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: Quint_624-12_35S::AT3G59940_9-day_seedlings_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT3G59940
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT3G59940
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.575393
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-ratio1.215057
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.969654
Spike_AFFX-r2-Bs-dap_5_signal65.733818
NoiseAvg:2.67,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_signal21.212088
#P15162
Spike_AFFX-r2-Bs-phe_M_signal56.489719
Corner-Avg:14418,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal38.942211
Spike_AFFX-r2-Ec-bioB_3_signal26.023169
Spike_AFFX-r2-Bs-lys_M_signal25.746481
Spike_AFFX-r2-P1-cre_3_signal5002.133301
Spike_AFFX-r2-Bs-lys_3-5-ratio1.629851
Spike_AFFX-r2-Bs-dap_M_signal224.195648
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.841805
Spike_AFFX-r2-Ec-bioB_avg-signal30.600988
Spike_AFFX-r2-Bs-thr_avg-signal71.979637
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1237.551758
Spike_AFFX-r2-Bs-phe_5_signal48.455315
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1673.363281
RawQ2.457789
Spike_AFFX-r2-Bs-lys_5_signal29.553234
Signal(A)4.031791
%A31.885138
Signal(All)145.512817
Corner+Avg:239,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal313.358124
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal70.327644
Spike_AFFX-r2-Ec-bioD_avg-signal1455.457520
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.470848
Spike_AFFX-r2-Bs-lys_avg-signal34.489029
Spike_AFFX-r2-P1-cre_avg-signal4559.460938
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_signal145.128967
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-signal58.424225
Spike_AFFX-r2-Bs-dap_3_signal459.896667
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.352156
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal309.880798
#M375
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.167366
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.011222
Spike_AFFX-r2-Bs-thr_M_signal49.597866
Signal(P)216.596954
Spike_AFFX-r2-Bs-phe_3-5-ratio1.451392
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11498,Count:9
Spike_AFFX-r2-P1-cre_5_signal4116.789063
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7273
Signal(M)15.416737
BackgroundAvg:58.77,Std:0.28,Min:58.0,Max:59.3
Spike_AFFX-r2-Ec-bioC_avg-signal311.619446
Spike_AFFX-r2-Bs-dap_avg-signal249.942032
Spike_AFFX-r2-Bs-dap_3-5-ratio6.996348
Spike_AFFX-r2-Ec-bioB_5_signal26.837587
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.575393
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-13_Col-0_9-day_seedlings_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 ("Quint_624-13_Col-0_9-day_seedlings_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: Quint_624-13_Col-0_9-day_seedlings_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.351469
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-ratio1.297122
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.299983
Spike_AFFX-r2-Bs-dap_5_signal85.259254
NoiseAvg:3.73,Std:0.12,Min:3.4,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_signal20.651751
#P15541
Spike_AFFX-r2-Bs-phe_M_signal49.627445
Corner-Avg:13507,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal57.409794
Spike_AFFX-r2-Ec-bioB_3_signal55.320892
Spike_AFFX-r2-Bs-lys_M_signal24.470737
Spike_AFFX-r2-P1-cre_3_signal3273.846924
Spike_AFFX-r2-Bs-lys_3-5-ratio1.919895
Spike_AFFX-r2-Bs-dap_M_signal305.439056
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.057598
Spike_AFFX-r2-Ec-bioB_avg-signal51.761921
Spike_AFFX-r2-Bs-thr_avg-signal81.610519
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal631.212097
Spike_AFFX-r2-Bs-phe_5_signal39.949512
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal931.882385
RawQ2.834636
Spike_AFFX-r2-Bs-lys_5_signal29.956547
Signal(A)4.212657
%A30.241123
Signal(All)138.068359
Corner+Avg:253,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal189.820496
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal77.212570
Spike_AFFX-r2-Ec-bioD_avg-signal781.547241
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.132401
Spike_AFFX-r2-Bs-lys_avg-signal37.313568
Spike_AFFX-r2-P1-cre_avg-signal2898.889648
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal166.403503
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-signal55.596508
Spike_AFFX-r2-Bs-dap_3_signal534.848083
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.476338
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal186.205215
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.513416
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.019416
Spike_AFFX-r2-Bs-thr_M_signal57.776306
Signal(P)200.413498
Spike_AFFX-r2-Bs-phe_3-5-ratio1.932754
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10770,Count:9
Spike_AFFX-r2-P1-cre_5_signal2523.932129
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6898
Signal(M)15.240645
BackgroundAvg:71.55,Std:0.83,Min:70.0,Max:74.4
Spike_AFFX-r2-Ec-bioC_avg-signal188.012848
Spike_AFFX-r2-Bs-dap_avg-signal308.515472
Spike_AFFX-r2-Bs-dap_3-5-ratio6.273197
Spike_AFFX-r2-Ec-bioB_5_signal42.555084
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.351469
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-14_Col-0_9-day_seedlings_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 ("Quint_624-14_Col-0_9-day_seedlings_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: Quint_624-14_Col-0_9-day_seedlings_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.487278
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-ratio1.184750
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.107169
Spike_AFFX-r2-Bs-dap_5_signal106.786850
NoiseAvg:3.32,Std:0.10,Min:3.1,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_signal24.539160
#P15179
Spike_AFFX-r2-Bs-phe_M_signal58.878117
Corner-Avg:9323,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.056839
Spike_AFFX-r2-Ec-bioB_3_signal72.142914
Spike_AFFX-r2-Bs-lys_M_signal37.135090
Spike_AFFX-r2-P1-cre_3_signal3644.656982
Spike_AFFX-r2-Bs-lys_3-5-ratio1.707680
Spike_AFFX-r2-Bs-dap_M_signal370.306000
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.465152
Spike_AFFX-r2-Ec-bioB_avg-signal73.786522
Spike_AFFX-r2-Bs-thr_avg-signal134.280258
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal747.264160
Spike_AFFX-r2-Bs-phe_5_signal48.808506
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1143.043213
RawQ2.746281
Spike_AFFX-r2-Bs-lys_5_signal39.655922
Signal(A)4.717786
%A31.784306
Signal(All)139.899948
Corner+Avg:176,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal219.064774
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal76.594917
Spike_AFFX-r2-Ec-bioD_avg-signal945.153687
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.545372
Spike_AFFX-r2-Bs-lys_avg-signal48.170216
Spike_AFFX-r2-P1-cre_avg-signal3360.483398
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_signal281.345184
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-signal61.427181
Spike_AFFX-r2-Bs-dap_3_signal571.601318
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.529637
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal220.325043
#M381
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal67.719643
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.994280
Spike_AFFX-r2-Bs-thr_M_signal96.956429
Signal(P)207.553360
Spike_AFFX-r2-Bs-phe_3-5-ratio1.569294
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6435,Count:9
Spike_AFFX-r2-P1-cre_5_signal3076.309814
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7250
Signal(M)16.959236
BackgroundAvg:67.56,Std:0.31,Min:66.4,Max:68.6
Spike_AFFX-r2-Ec-bioC_avg-signal219.694916
Spike_AFFX-r2-Bs-dap_avg-signal349.564728
Spike_AFFX-r2-Bs-dap_3-5-ratio5.352731
Spike_AFFX-r2-Ec-bioB_5_signal65.159805
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.487278
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-15_Col-0_9-day_seedlings_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 ("Quint_624-15_Col-0_9-day_seedlings_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: Quint_624-15_Col-0_9-day_seedlings_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.46879
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-ratio1.205928
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.227220
Spike_AFFX-r2-Bs-dap_5_signal71.120087
NoiseAvg:3.21,Std:0.10,Min:3.0,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_signal25.566710
#P15050
Spike_AFFX-r2-Bs-phe_M_signal46.266499
Corner-Avg:7554,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal70.311722
Spike_AFFX-r2-Ec-bioB_3_signal61.449047
Spike_AFFX-r2-Bs-lys_M_signal20.772129
Spike_AFFX-r2-P1-cre_3_signal3405.763672
Spike_AFFX-r2-Bs-lys_3-5-ratio2.290754
Spike_AFFX-r2-Bs-dap_M_signal312.942078
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.436855
Spike_AFFX-r2-Ec-bioB_avg-signal60.610840
Spike_AFFX-r2-Bs-thr_avg-signal86.980171
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal666.420471
Spike_AFFX-r2-Bs-phe_5_signal32.113972
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal943.341553
RawQ2.651315
Spike_AFFX-r2-Bs-lys_5_signal24.446781
Signal(A)4.763429
%A32.135029
Signal(All)140.130661
Corner+Avg:138,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal222.929016
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.095238
Spike_AFFX-r2-Ec-bioD_avg-signal804.880981
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.979836
Spike_AFFX-r2-Bs-lys_avg-signal33.740158
Spike_AFFX-r2-P1-cre_avg-signal3114.974609
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_signal164.569199
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-signal46.491901
Spike_AFFX-r2-Bs-dap_3_signal499.716705
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.415535
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal196.629242
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.001568
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.133753
Spike_AFFX-r2-Bs-thr_M_signal70.804604
Signal(P)209.534729
Spike_AFFX-r2-Bs-phe_3-5-ratio1.902450
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5881,Count:9
Spike_AFFX-r2-P1-cre_5_signal2824.185303
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7330
Signal(M)18.526924
BackgroundAvg:64.00,Std:0.47,Min:62.8,Max:65.2
Spike_AFFX-r2-Ec-bioC_avg-signal209.779129
Spike_AFFX-r2-Bs-dap_avg-signal294.592987
Spike_AFFX-r2-Bs-dap_3-5-ratio7.026379
Spike_AFFX-r2-Ec-bioB_5_signal50.071747
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.468790
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-16_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_seedlings_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 ("Quint_624-16_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_seedlings_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: Quint_624-16_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_seedlings_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: AT1G15670-1/AT1G80440-1/AT3G59940-1
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G15670,AT1G80440,AT3G59940
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.397753
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-ratio1.168533
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.950665
Spike_AFFX-r2-Bs-dap_5_signal76.615715
NoiseAvg:3.62,Std:0.10,Min:3.3,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.529497
#P15412
Spike_AFFX-r2-Bs-phe_M_signal39.740665
Corner-Avg:9055,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.318085
Spike_AFFX-r2-Ec-bioB_3_signal54.736855
Spike_AFFX-r2-Bs-lys_M_signal25.415356
Spike_AFFX-r2-P1-cre_3_signal3036.516113
Spike_AFFX-r2-Bs-lys_3-5-ratio2.077064
Spike_AFFX-r2-Bs-dap_M_signal277.087524
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.879419
Spike_AFFX-r2-Ec-bioB_avg-signal60.210785
Spike_AFFX-r2-Bs-thr_avg-signal81.531265
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal587.767456
Spike_AFFX-r2-Bs-phe_5_signal26.582098
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal889.135376
RawQ2.924271
Spike_AFFX-r2-Bs-lys_5_signal28.360342
Signal(A)4.318701
%A30.797895
Signal(All)137.614487
Corner+Avg:168,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal195.362076
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal65.743866
Spike_AFFX-r2-Ec-bioD_avg-signal738.451416
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.566856
Spike_AFFX-r2-Bs-lys_avg-signal37.560650
Spike_AFFX-r2-P1-cre_avg-signal2817.543213
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_signal154.989853
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-signal44.022205
Spike_AFFX-r2-Bs-dap_3_signal416.392578
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.512733
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal188.650803
#M373
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal58.906254
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.035575
Spike_AFFX-r2-Bs-thr_M_signal67.074440
Signal(P)201.315582
Spike_AFFX-r2-Bs-phe_3-5-ratio2.473238
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7493,Count:9
Spike_AFFX-r2-P1-cre_5_signal2598.570313
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7025
Signal(M)16.010139
BackgroundAvg:74.74,Std:0.71,Min:72.7,Max:76.1
Spike_AFFX-r2-Ec-bioC_avg-signal192.006439
Spike_AFFX-r2-Bs-dap_avg-signal256.698608
Spike_AFFX-r2-Bs-dap_3-5-ratio5.434819
Spike_AFFX-r2-Ec-bioB_5_signal57.577408
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.397753
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-17_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_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 ("Quint_624-17_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_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: Quint_624-17_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: AT1G15670-1/AT1G80440-1/AT3G59940-1
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G15670,AT1G80440,AT3G59940
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.298124
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-ratio1.220665
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.972876
Spike_AFFX-r2-Bs-dap_5_signal46.270615
NoiseAvg:3.97,Std:0.11,Min:3.7,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.138665
#P15524
Spike_AFFX-r2-Bs-phe_M_signal31.633888
Corner-Avg:10513,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal58.143982
Spike_AFFX-r2-Ec-bioB_3_signal44.222721
Spike_AFFX-r2-Bs-lys_M_signal16.563162
Spike_AFFX-r2-P1-cre_3_signal2567.048340
Spike_AFFX-r2-Bs-lys_3-5-ratio2.423719
Spike_AFFX-r2-Bs-dap_M_signal185.139297
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.750109
Spike_AFFX-r2-Ec-bioB_avg-signal49.274120
Spike_AFFX-r2-Bs-thr_avg-signal51.164684
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal477.659271
Spike_AFFX-r2-Bs-phe_5_signal20.687756
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal685.959900
RawQ3.105394
Spike_AFFX-r2-Bs-lys_5_signal19.480227
Signal(A)3.849010
%A30.201666
Signal(All)135.982117
Corner+Avg:193,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal155.026352
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.713356
Spike_AFFX-r2-Ec-bioD_avg-signal581.809570
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.057869
Spike_AFFX-r2-Bs-lys_avg-signal27.752661
Spike_AFFX-r2-P1-cre_avg-signal2335.020020
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.740465
Spike_AFFX-r2-Bs-thr_3_signal102.187645
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-signal35.011669
Spike_AFFX-r2-Bs-dap_3_signal310.448517
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.436086
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal143.310699
#M397
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.214596
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.081750
Spike_AFFX-r2-Bs-thr_M_signal36.167725
Signal(P)197.716568
Spike_AFFX-r2-Bs-phe_3-5-ratio2.548046
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8593,Count:9
Spike_AFFX-r2-P1-cre_5_signal2102.991943
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6889
Signal(M)14.821838
BackgroundAvg:78.19,Std:0.66,Min:76.3,Max:79.7
Spike_AFFX-r2-Ec-bioC_avg-signal149.168518
Spike_AFFX-r2-Bs-dap_avg-signal180.619492
Spike_AFFX-r2-Bs-dap_3-5-ratio6.709410
Spike_AFFX-r2-Ec-bioB_5_signal45.455650
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.298124
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-18_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_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 ("Quint_624-18_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_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: Quint_624-18_AT1G15670-1/AT1G80440-1/AT3G59940-1_9-day_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: AT1G15670-1/AT1G80440-1/AT3G59940-1
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G15670,AT1G80440,AT3G59940
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.44523
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-ratio1.169649
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.051527
Spike_AFFX-r2-Bs-dap_5_signal49.630417
NoiseAvg:3.39,Std:0.09,Min:3.2,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_signal13.127984
#P15176
Spike_AFFX-r2-Bs-phe_M_signal38.288273
Corner-Avg:8395,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.678734
Spike_AFFX-r2-Ec-bioB_3_signal55.004532
Spike_AFFX-r2-Bs-lys_M_signal14.603337
Spike_AFFX-r2-P1-cre_3_signal3198.199463
Spike_AFFX-r2-Bs-lys_3-5-ratio2.567246
Spike_AFFX-r2-Bs-dap_M_signal211.329193
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.251082
Spike_AFFX-r2-Ec-bioB_avg-signal57.997486
Spike_AFFX-r2-Bs-thr_avg-signal54.882935
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal624.767212
Spike_AFFX-r2-Bs-phe_5_signal21.953203
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal915.338257
RawQ2.731803
Spike_AFFX-r2-Bs-lys_5_signal20.203552
Signal(A)4.614820
%A31.814993
Signal(All)140.199661
Corner+Avg:189,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal209.019470
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.363453
Spike_AFFX-r2-Ec-bioD_avg-signal770.052734
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.532219
Spike_AFFX-r2-Bs-lys_avg-signal28.891459
Spike_AFFX-r2-P1-cre_avg-signal2966.261230
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.652784
Spike_AFFX-r2-Bs-thr_3_signal108.320084
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-signal35.534977
Spike_AFFX-r2-Bs-dap_3_signal307.999939
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.465087
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal194.658157
#M377
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal51.867485
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.073777
Spike_AFFX-r2-Bs-thr_M_signal43.200726
Signal(P)208.080536
Spike_AFFX-r2-Bs-phe_3-5-ratio2.111922
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6626,Count:9
Spike_AFFX-r2-P1-cre_5_signal2734.323242
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7257
Signal(M)17.597456
BackgroundAvg:69.02,Std:1.10,Min:66.8,Max:71.2
Spike_AFFX-r2-Ec-bioC_avg-signal201.838806
Spike_AFFX-r2-Bs-dap_avg-signal189.653183
Spike_AFFX-r2-Bs-dap_3-5-ratio6.205871
Spike_AFFX-r2-Ec-bioB_5_signal52.309196
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.445230
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-19_35S::AT1G15670_Flowers_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 ("Quint_624-19_35S::AT1G15670_Flowers_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: Quint_624-19_35S::AT1G15670_Flowers_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G15670
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in At1g15670
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.386955
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-ratio1.103529
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.916570
Spike_AFFX-r2-Bs-dap_5_signal11.452881
NoiseAvg:3.78,Std:0.09,Min:3.6,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.050583
#P15353
Spike_AFFX-r2-Bs-phe_M_signal13.847800
Corner-Avg:8035,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.620842
Spike_AFFX-r2-Ec-bioB_3_signal55.509155
Spike_AFFX-r2-Bs-lys_M_signal10.677662
Spike_AFFX-r2-P1-cre_3_signal3119.777100
Spike_AFFX-r2-Bs-lys_3-5-ratio4.124957
Spike_AFFX-r2-Bs-dap_M_signal71.061775
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio20.829741
Spike_AFFX-r2-Ec-bioB_avg-signal61.563934
Spike_AFFX-r2-Bs-thr_avg-signal28.203894
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal648.128662
Spike_AFFX-r2-Bs-phe_5_signal12.971571
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1051.433716
RawQ2.894279
Spike_AFFX-r2-Bs-lys_5_signal9.601891
Signal(A)4.728800
%A30.832968
Signal(All)136.444107
Corner+Avg:228,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal207.443832
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.955784
Spike_AFFX-r2-Ec-bioD_avg-signal849.781189
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.308197
Spike_AFFX-r2-Bs-lys_avg-signal19.962313
Spike_AFFX-r2-P1-cre_avg-signal2973.433594
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.858834
Spike_AFFX-r2-Bs-thr_3_signal63.542843
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-signal18.925051
Spike_AFFX-r2-Bs-dap_3_signal178.528656
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.622261
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal200.357391
#M424
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.607388
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.035369
Spike_AFFX-r2-Bs-thr_M_signal18.018251
Signal(P)200.066208
Spike_AFFX-r2-Bs-phe_3-5-ratio2.309341
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7025,Count:9
Spike_AFFX-r2-P1-cre_5_signal2827.090088
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7033
Signal(M)17.490696
BackgroundAvg:73.81,Std:1.10,Min:71.2,Max:76.7
Spike_AFFX-r2-Ec-bioC_avg-signal203.900604
Spike_AFFX-r2-Bs-dap_avg-signal87.014435
Spike_AFFX-r2-Bs-dap_3-5-ratio15.588100
Spike_AFFX-r2-Ec-bioB_5_signal60.561802
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.386955
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-20_35S::AT1G15670_Flowers_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 ("Quint_624-20_35S::AT1G15670_Flowers_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: Quint_624-20_35S::AT1G15670_Flowers_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G15670
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in At1g15670
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.260905
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-ratio1.230102
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.149853
Spike_AFFX-r2-Bs-dap_5_signal32.628773
NoiseAvg:4.41,Std:0.16,Min:4.1,Max:5.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.571991
#P15818
Spike_AFFX-r2-Bs-phe_M_signal19.382521
Corner-Avg:10736,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal55.631847
Spike_AFFX-r2-Ec-bioB_3_signal51.900295
Spike_AFFX-r2-Bs-lys_M_signal11.425768
Spike_AFFX-r2-P1-cre_3_signal2570.803955
Spike_AFFX-r2-Bs-lys_3-5-ratio3.539867
Spike_AFFX-r2-Bs-dap_M_signal115.057365
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.300731
Spike_AFFX-r2-Ec-bioB_avg-signal50.889538
Spike_AFFX-r2-Bs-thr_avg-signal27.984400
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal511.781067
Spike_AFFX-r2-Bs-phe_5_signal14.028408
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal693.604431
RawQ3.199332
Spike_AFFX-r2-Bs-lys_5_signal12.276982
Signal(A)3.563008
%A29.026743
Signal(All)131.430740
Corner+Avg:199,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal151.782135
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.001755
Spike_AFFX-r2-Ec-bioD_avg-signal602.692749
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.346779
Spike_AFFX-r2-Bs-lys_avg-signal22.387215
Spike_AFFX-r2-P1-cre_avg-signal2330.357178
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal45.437820
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-signal22.137564
Spike_AFFX-r2-Bs-dap_3_signal239.805298
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.355276
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal154.139938
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.458889
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.984703
Spike_AFFX-r2-Bs-thr_M_signal29.943390
Signal(P)187.716965
Spike_AFFX-r2-Bs-phe_3-5-ratio2.352495
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8423,Count:9
Spike_AFFX-r2-P1-cre_5_signal2089.910400
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6621
Signal(M)13.578625
BackgroundAvg:84.37,Std:0.75,Min:82.3,Max:86.5
Spike_AFFX-r2-Ec-bioC_avg-signal152.961029
Spike_AFFX-r2-Bs-dap_avg-signal129.163818
Spike_AFFX-r2-Bs-dap_3-5-ratio7.349504
Spike_AFFX-r2-Ec-bioB_5_signal45.136467
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.260905
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-21_35S::AT1G15670_Flowers_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 ("Quint_624-21_35S::AT1G15670_Flowers_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: Quint_624-21_35S::AT1G15670_Flowers_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G15670
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in At1g15670
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.345871
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-ratio1.278225
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.944281
Spike_AFFX-r2-Bs-dap_5_signal30.238304
NoiseAvg:3.79,Std:0.06,Min:3.5,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_signal5.898503
#P15610
Spike_AFFX-r2-Bs-phe_M_signal18.948690
Corner-Avg:8802,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal56.573868
Spike_AFFX-r2-Ec-bioB_3_signal38.269531
Spike_AFFX-r2-Bs-lys_M_signal11.623390
Spike_AFFX-r2-P1-cre_3_signal2428.107178
Spike_AFFX-r2-Bs-lys_3-5-ratio2.730339
Spike_AFFX-r2-Bs-dap_M_signal95.283867
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.872343
Spike_AFFX-r2-Ec-bioB_avg-signal45.123692
Spike_AFFX-r2-Bs-thr_avg-signal27.586237
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal453.332031
Spike_AFFX-r2-Bs-phe_5_signal14.422462
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal639.116577
RawQ2.928335
Spike_AFFX-r2-Bs-lys_5_signal11.320924
Signal(A)3.948480
%A29.960543
Signal(All)133.250839
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal133.353073
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.349365
Spike_AFFX-r2-Ec-bioD_avg-signal546.224304
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.434898
Spike_AFFX-r2-Bs-lys_avg-signal17.951424
Spike_AFFX-r2-P1-cre_avg-signal2163.849854
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal58.232048
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-signal20.906839
Spike_AFFX-r2-Bs-dap_3_signal212.954346
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.409820
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal138.864517
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.909960
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.960311
Spike_AFFX-r2-Bs-thr_M_signal18.628160
Signal(P)192.645050
Spike_AFFX-r2-Bs-phe_3-5-ratio2.034976
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6787,Count:9
Spike_AFFX-r2-P1-cre_5_signal1899.592529
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6834
Signal(M)14.422466
BackgroundAvg:75.38,Std:0.94,Min:73.5,Max:78.5
Spike_AFFX-r2-Ec-bioC_avg-signal136.108795
Spike_AFFX-r2-Bs-dap_avg-signal112.825508
Spike_AFFX-r2-Bs-dap_3-5-ratio7.042536
Spike_AFFX-r2-Ec-bioB_5_signal40.527676
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.345871
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-22_35S::AT2G44130-Flowers_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 ("Quint_624-22_35S::AT2G44130-Flowers_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: Quint_624-22_35S::AT2G44130-Flowers_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT2G44130
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT2G44130
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.260301
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-ratio1.173591
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.367263
Spike_AFFX-r2-Bs-dap_5_signal16.755732
NoiseAvg:4.03,Std:0.13,Min:3.8,Max:4.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.371741
#P16092
Spike_AFFX-r2-Bs-phe_M_signal14.176458
Corner-Avg:9107,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal47.455738
Spike_AFFX-r2-Ec-bioB_3_signal42.484596
Spike_AFFX-r2-Bs-lys_M_signal10.376830
Spike_AFFX-r2-P1-cre_3_signal2232.034424
Spike_AFFX-r2-Bs-lys_3-5-ratio3.680475
Spike_AFFX-r2-Bs-dap_M_signal91.899872
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.217354
Spike_AFFX-r2-Ec-bioB_avg-signal40.337692
Spike_AFFX-r2-Bs-thr_avg-signal27.952629
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal427.772766
Spike_AFFX-r2-Bs-phe_5_signal10.996609
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal614.682495
RawQ3.046856
Spike_AFFX-r2-Bs-lys_5_signal7.347236
Signal(A)2.851704
%A27.996492
Signal(All)130.277847
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal133.780289
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.315250
Spike_AFFX-r2-Ec-bioD_avg-signal521.227661
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.548004
Spike_AFFX-r2-Bs-lys_avg-signal14.921795
Spike_AFFX-r2-P1-cre_avg-signal2066.959717
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.455502
Spike_AFFX-r2-Bs-thr_3_signal61.424206
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-signal18.496105
Spike_AFFX-r2-Bs-dap_3_signal209.053375
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.436937
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal134.765152
#M332
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.041319
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.992692
Spike_AFFX-r2-Bs-thr_M_signal19.061935
Signal(P)183.294312
Spike_AFFX-r2-Bs-phe_3-5-ratio2.756782
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7101,Count:9
Spike_AFFX-r2-P1-cre_5_signal1901.885010
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6386
Signal(M)11.610103
BackgroundAvg:78.76,Std:0.89,Min:76.7,Max:81.2
Spike_AFFX-r2-Ec-bioC_avg-signal134.272720
Spike_AFFX-r2-Bs-dap_avg-signal105.902992
Spike_AFFX-r2-Bs-dap_3-5-ratio12.476529
Spike_AFFX-r2-Ec-bioB_5_signal31.072735
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.260301
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-23_35S::AT2G44130-Flowers_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 ("Quint_624-23_35S::AT2G44130-Flowers_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: Quint_624-23_35S::AT2G44130-Flowers_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT2G44130
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT2G44130
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.433817
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-ratio1.248541
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.873408
Spike_AFFX-r2-Bs-dap_5_signal64.970116
NoiseAvg:3.37,Std:0.10,Min:3.1,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_signal12.641091
#P15634
Spike_AFFX-r2-Bs-phe_M_signal41.747444
Corner-Avg:7725,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal59.183586
Spike_AFFX-r2-Ec-bioB_3_signal50.854889
Spike_AFFX-r2-Bs-lys_M_signal22.606472
Spike_AFFX-r2-P1-cre_3_signal2784.121826
Spike_AFFX-r2-Bs-lys_3-5-ratio1.797636
Spike_AFFX-r2-Bs-dap_M_signal227.914200
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.075270
Spike_AFFX-r2-Ec-bioB_avg-signal56.088093
Spike_AFFX-r2-Bs-thr_avg-signal84.501839
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal447.599854
Spike_AFFX-r2-Bs-phe_5_signal49.958370
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal752.266296
RawQ2.868373
Spike_AFFX-r2-Bs-lys_5_signal30.667858
Signal(A)3.939336
%A29.872862
Signal(All)132.667175
Corner+Avg:131,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal168.720108
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.173721
Spike_AFFX-r2-Ec-bioD_avg-signal599.933105
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.540115
Spike_AFFX-r2-Bs-lys_avg-signal36.134659
Spike_AFFX-r2-P1-cre_avg-signal2507.011230
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.587023
Spike_AFFX-r2-Bs-thr_3_signal177.926773
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-signal51.293179
Spike_AFFX-r2-Bs-dap_3_signal443.221344
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.680667
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal169.077957
#M362
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal55.129639
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.997883
Spike_AFFX-r2-Bs-thr_M_signal62.937641
Signal(P)191.510300
Spike_AFFX-r2-Bs-phe_3-5-ratio1.244511
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6269,Count:9
Spike_AFFX-r2-P1-cre_5_signal2229.900635
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6814
Signal(M)14.430088
BackgroundAvg:73.47,Std:0.69,Min:71.1,Max:75.1
Spike_AFFX-r2-Ec-bioC_avg-signal168.899033
Spike_AFFX-r2-Bs-dap_avg-signal245.368546
Spike_AFFX-r2-Bs-dap_3-5-ratio6.821926
Spike_AFFX-r2-Ec-bioB_5_signal58.225811
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.433817
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-24_35S::AT2G44130-Flowers_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 ("Quint_624-24_35S::AT2G44130-Flowers_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: Quint_624-24_35S::AT2G44130-Flowers_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT2G44130
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT2G44130
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.399209
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-ratio1.300836
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.830906
Spike_AFFX-r2-Bs-dap_5_signal9.905634
NoiseAvg:3.79,Std:0.12,Min:3.5,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.626513
#P15422
Spike_AFFX-r2-Bs-phe_M_signal13.327019
Corner-Avg:7298,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal59.011192
Spike_AFFX-r2-Ec-bioB_3_signal40.565826
Spike_AFFX-r2-Bs-lys_M_signal10.225575
Spike_AFFX-r2-P1-cre_3_signal2862.449463
Spike_AFFX-r2-Bs-lys_3-5-ratio3.343632
Spike_AFFX-r2-Bs-dap_M_signal92.473984
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.792034
Spike_AFFX-r2-Ec-bioB_avg-signal49.466064
Spike_AFFX-r2-Bs-thr_avg-signal29.897932
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal543.010864
Spike_AFFX-r2-Bs-phe_5_signal11.714285
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal792.422668
RawQ2.946049
Spike_AFFX-r2-Bs-lys_5_signal9.653985
Signal(A)4.387928
%A30.675142
Signal(All)134.124695
Corner+Avg:132,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal179.729156
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.395775
Spike_AFFX-r2-Ec-bioD_avg-signal667.716797
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.610695
Spike_AFFX-r2-Bs-lys_avg-signal17.386311
Spike_AFFX-r2-P1-cre_avg-signal2531.458984
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.714160
Spike_AFFX-r2-Bs-thr_3_signal66.348030
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-signal16.812361
Spike_AFFX-r2-Bs-dap_3_signal165.392426
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.459313
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.914017
#M391
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.279373
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.987990
Spike_AFFX-r2-Bs-thr_M_signal17.719252
Signal(P)195.998886
Spike_AFFX-r2-Bs-phe_3-5-ratio2.167932
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5643,Count:9
Spike_AFFX-r2-P1-cre_5_signal2200.468750
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6997
Signal(M)15.312870
BackgroundAvg:77.85,Std:0.81,Min:75.2,Max:79.9
Spike_AFFX-r2-Ec-bioC_avg-signal180.821594
Spike_AFFX-r2-Bs-dap_avg-signal89.257347
Spike_AFFX-r2-Bs-dap_3-5-ratio16.696804
Spike_AFFX-r2-Ec-bioB_5_signal48.821171
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.399209
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-25_35S::AT1G80440-Flowers_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 ("Quint_624-25_35S::AT1G80440-Flowers_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: Quint_624-25_35S::AT1G80440-Flowers_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G80440
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G80440
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.348685
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-ratio1.267010
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.686014
Spike_AFFX-r2-Bs-dap_5_signal29.088539
NoiseAvg:4.05,Std:0.18,Min:3.7,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_signal3.764586
#P15702
Spike_AFFX-r2-Bs-phe_M_signal18.719301
Corner-Avg:11865,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal13.775018
Spike_AFFX-r2-Ec-bioB_3_signal10.558066
Spike_AFFX-r2-Bs-lys_M_signal13.724277
Spike_AFFX-r2-P1-cre_3_signal3345.079346
Spike_AFFX-r2-Bs-lys_3-5-ratio2.644384
Spike_AFFX-r2-Bs-dap_M_signal105.537430
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.786875
Spike_AFFX-r2-Ec-bioB_avg-signal13.241177
Spike_AFFX-r2-Bs-thr_avg-signal32.874596
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal708.139465
Spike_AFFX-r2-Bs-phe_5_signal13.582553
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1082.466553
RawQ3.044288
Spike_AFFX-r2-Bs-lys_5_signal9.740691
Signal(A)3.532695
%A29.592283
Signal(All)133.524567
Corner+Avg:211,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal172.538162
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.447557
Spike_AFFX-r2-Ec-bioD_avg-signal895.302979
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.838226
Spike_AFFX-r2-Bs-lys_avg-signal16.407700
Spike_AFFX-r2-P1-cre_avg-signal2992.607910
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_signal70.724808
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-signal19.916471
Spike_AFFX-r2-Bs-dap_3_signal231.147446
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.528606
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal208.793030
#M358
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.758127
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.826360
Spike_AFFX-r2-Bs-thr_M_signal24.134390
Signal(P)192.117630
Spike_AFFX-r2-Bs-phe_3-5-ratio2.020795
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10064,Count:9
Spike_AFFX-r2-P1-cre_5_signal2640.136475
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6750
Signal(M)14.577607
BackgroundAvg:75.04,Std:0.68,Min:73.7,Max:76.5
Spike_AFFX-r2-Ec-bioC_avg-signal190.665588
Spike_AFFX-r2-Bs-dap_avg-signal121.924469
Spike_AFFX-r2-Bs-dap_3-5-ratio7.946341
Spike_AFFX-r2-Ec-bioB_5_signal15.390445
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.348685
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-26_35S::AT1G80440-Flowers_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 ("Quint_624-26_35S::AT1G80440-Flowers_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: Quint_624-26_35S::AT1G80440-Flowers_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G80440
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G80440
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.425933
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-ratio1.243102
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.670935
Spike_AFFX-r2-Bs-dap_5_signal44.571785
NoiseAvg:3.47,Std:0.06,Min:3.3,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_signal7.483550
#P15700
Spike_AFFX-r2-Bs-phe_M_signal33.864510
Corner-Avg:12776,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal16.237814
Spike_AFFX-r2-Ec-bioB_3_signal12.167192
Spike_AFFX-r2-Bs-lys_M_signal18.051569
Spike_AFFX-r2-P1-cre_3_signal3615.805176
Spike_AFFX-r2-Bs-lys_3-5-ratio2.307760
Spike_AFFX-r2-Bs-dap_M_signal182.035660
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.484865
Spike_AFFX-r2-Ec-bioB_avg-signal15.513230
Spike_AFFX-r2-Bs-thr_avg-signal51.424526
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal755.131287
Spike_AFFX-r2-Bs-phe_5_signal29.617897
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1179.176758
RawQ2.958842
Spike_AFFX-r2-Bs-lys_5_signal19.081533
Signal(A)3.536567
%A29.833406
Signal(All)133.765778
Corner+Avg:227,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal178.575943
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal54.382263
Spike_AFFX-r2-Ec-bioD_avg-signal967.154053
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.829460
Spike_AFFX-r2-Bs-lys_avg-signal27.056236
Spike_AFFX-r2-P1-cre_avg-signal3262.250244
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.337133
Spike_AFFX-r2-Bs-thr_3_signal115.881767
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-signal39.288223
Spike_AFFX-r2-Bs-dap_3_signal351.414032
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.561552
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal234.720078
#M305
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.035603
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.760804
Spike_AFFX-r2-Bs-thr_M_signal30.908255
Signal(P)192.537354
Spike_AFFX-r2-Bs-phe_3-5-ratio1.836128
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9637,Count:9
Spike_AFFX-r2-P1-cre_5_signal2908.695313
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6805
Signal(M)14.080370
BackgroundAvg:71.93,Std:0.40,Min:70.8,Max:73.0
Spike_AFFX-r2-Ec-bioC_avg-signal206.648010
Spike_AFFX-r2-Bs-dap_avg-signal192.673828
Spike_AFFX-r2-Bs-dap_3-5-ratio7.884226
Spike_AFFX-r2-Ec-bioB_5_signal18.134686
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.425933
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-27_35S::AT1G80440-Flowers_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 ("Quint_624-27_35S::AT1G80440-Flowers_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: Quint_624-27_35S::AT1G80440-Flowers_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT1G80440
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT1G80440
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.513619
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-ratio1.167695
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.484865
Spike_AFFX-r2-Bs-dap_5_signal17.723181
NoiseAvg:3.79,Std:0.11,Min:3.3,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_signal7.925915
#P15162
Spike_AFFX-r2-Bs-phe_M_signal11.829084
Corner-Avg:10315,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal21.218002
Spike_AFFX-r2-Ec-bioB_3_signal10.501657
Spike_AFFX-r2-Bs-lys_M_signal13.126715
Spike_AFFX-r2-P1-cre_3_signal3561.494873
Spike_AFFX-r2-Bs-lys_3-5-ratio2.364368
Spike_AFFX-r2-Bs-dap_M_signal66.197372
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.324527
Spike_AFFX-r2-Ec-bioB_avg-signal17.792864
Spike_AFFX-r2-Bs-thr_avg-signal19.053558
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal722.142273
Spike_AFFX-r2-Bs-phe_5_signal14.662983
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1143.914185
RawQ3.182053
Spike_AFFX-r2-Bs-lys_5_signal10.597979
Signal(A)4.881633
%A31.871986
Signal(All)135.808670
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal192.240692
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.918619
Spike_AFFX-r2-Ec-bioD_avg-signal933.028198
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.470848
Spike_AFFX-r2-Bs-lys_avg-signal16.260736
Spike_AFFX-r2-P1-cre_avg-signal3305.758301
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_signal34.275837
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-signal16.803562
Spike_AFFX-r2-Bs-dap_3_signal172.025803
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.584056
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal200.602142
#M378
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.057520
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.958318
Spike_AFFX-r2-Bs-thr_M_signal14.958922
Signal(P)201.525009
Spike_AFFX-r2-Bs-phe_3-5-ratio1.631225
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9055,Count:9
Spike_AFFX-r2-P1-cre_5_signal3050.021973
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7270
Signal(M)17.946775
BackgroundAvg:81.37,Std:0.64,Min:79.6,Max:83.3
Spike_AFFX-r2-Ec-bioC_avg-signal196.421417
Spike_AFFX-r2-Bs-dap_avg-signal85.315453
Spike_AFFX-r2-Bs-dap_3-5-ratio9.706260
Spike_AFFX-r2-Ec-bioB_5_signal21.658934
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.513619
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-28_35S::AT3G59940-Flowers_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 ("Quint_624-28_35S::AT3G59940-Flowers_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: Quint_624-28_35S::AT3G59940-Flowers_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT3G59940
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT3G59940
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.420922
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-ratio1.247694
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.998219
Spike_AFFX-r2-Bs-dap_5_signal28.721085
NoiseAvg:3.57,Std:0.08,Min:3.4,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_signal6.409104
#P15702
Spike_AFFX-r2-Bs-phe_M_signal20.787720
Corner-Avg:10008,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.800242
Spike_AFFX-r2-Ec-bioB_3_signal14.845873
Spike_AFFX-r2-Bs-lys_M_signal7.933334
Spike_AFFX-r2-P1-cre_3_signal3337.041992
Spike_AFFX-r2-Bs-lys_3-5-ratio3.553949
Spike_AFFX-r2-Bs-dap_M_signal94.192993
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.010495
Spike_AFFX-r2-Ec-bioB_avg-signal13.506158
Spike_AFFX-r2-Bs-thr_avg-signal30.615381
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal647.177734
Spike_AFFX-r2-Bs-phe_5_signal12.408172
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal851.278259
RawQ2.985301
Spike_AFFX-r2-Bs-lys_5_signal8.046036
Signal(A)3.959390
%A29.631741
Signal(All)133.144043
Corner+Avg:169,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal191.917160
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.118938
Spike_AFFX-r2-Ec-bioD_avg-signal749.228027
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.838226
Spike_AFFX-r2-Bs-lys_avg-signal14.858190
Spike_AFFX-r2-P1-cre_avg-signal3005.804688
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.530031
Spike_AFFX-r2-Bs-thr_3_signal64.158310
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-signal21.771608
Spike_AFFX-r2-Bs-dap_3_signal207.698212
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.315370
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal183.352280
#M349
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.595201
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.046713
Spike_AFFX-r2-Bs-thr_M_signal21.278736
Signal(P)191.368164
Spike_AFFX-r2-Bs-phe_3-5-ratio2.588531
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9210,Count:9
Spike_AFFX-r2-P1-cre_5_signal2674.567139
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6759
Signal(M)15.447739
BackgroundAvg:71.37,Std:0.69,Min:69.6,Max:73.2
Spike_AFFX-r2-Ec-bioC_avg-signal187.634720
Spike_AFFX-r2-Bs-dap_avg-signal110.204102
Spike_AFFX-r2-Bs-dap_3-5-ratio7.231559
Spike_AFFX-r2-Ec-bioB_5_signal14.872359
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.420922
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-29_35S::AT3G59940-Flowers_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 ("Quint_624-29_35S::AT3G59940-Flowers_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: Quint_624-29_35S::AT3G59940-Flowers_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT3G59940
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT3G59940
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.421319
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-ratio1.055924
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.831917
Spike_AFFX-r2-Bs-dap_5_signal19.336254
NoiseAvg:3.67,Std:0.11,Min:3.2,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_signal3.697864
#P15671
Spike_AFFX-r2-Bs-phe_M_signal14.023704
Corner-Avg:10216,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal16.775270
Spike_AFFX-r2-Ec-bioB_3_signal15.146314
Spike_AFFX-r2-Bs-lys_M_signal10.107183
Spike_AFFX-r2-P1-cre_3_signal2737.926025
Spike_AFFX-r2-Bs-lys_3-5-ratio2.912830
Spike_AFFX-r2-Bs-dap_M_signal95.968971
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.569864
Spike_AFFX-r2-Ec-bioB_avg-signal16.709368
Spike_AFFX-r2-Bs-thr_avg-signal24.601320
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal581.039734
Spike_AFFX-r2-Bs-phe_5_signal8.882747
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal854.432434
RawQ2.952346
Spike_AFFX-r2-Bs-lys_5_signal8.552081
Signal(A)3.922263
%A29.530907
Signal(All)133.072495
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal168.244843
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.367542
Spike_AFFX-r2-Ec-bioD_avg-signal717.736084
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.702324
Spike_AFFX-r2-Bs-lys_avg-signal14.523339
Spike_AFFX-r2-P1-cre_avg-signal2665.423340
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.766769
Spike_AFFX-r2-Bs-thr_3_signal46.481644
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-signal15.424664
Spike_AFFX-r2-Bs-dap_3_signal174.115952
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.470523
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal173.925461
#M403
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.910755
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.967339
Spike_AFFX-r2-Bs-thr_M_signal23.624458
Signal(P)191.645020
Spike_AFFX-r2-Bs-phe_3-5-ratio2.630666
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9339,Count:9
Spike_AFFX-r2-P1-cre_5_signal2592.920410
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6736
Signal(M)14.129635
BackgroundAvg:75.63,Std:1.05,Min:73.0,Max:77.9
Spike_AFFX-r2-Ec-bioC_avg-signal171.085144
Spike_AFFX-r2-Bs-dap_avg-signal96.473724
Spike_AFFX-r2-Bs-dap_3-5-ratio9.004637
Spike_AFFX-r2-Ec-bioB_5_signal18.206516
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.421319
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-30_35S::AT3G59940-Flowers_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 ("Quint_624-30_35S::AT3G59940-Flowers_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: Quint_624-30_35S::AT3G59940-Flowers_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT3G59940
Stock Code:
Genetic Background: Col-0
Age: 9 day
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT3G59940
Tissue: whole plant
Additional Organism Information:
Sample Description9 day old seedlings
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:0.347855
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-ratio1.216055
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.849454
Spike_AFFX-r2-Bs-dap_5_signal30.853355
NoiseAvg:3.72,Std:0.08,Min:3.4,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.922013
#P16002
Spike_AFFX-r2-Bs-phe_M_signal21.974539
Corner-Avg:10486,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal11.131583
Spike_AFFX-r2-Ec-bioB_3_signal12.068385
Spike_AFFX-r2-Bs-lys_M_signal16.014503
Spike_AFFX-r2-P1-cre_3_signal3073.661621
Spike_AFFX-r2-Bs-lys_3-5-ratio2.619881
Spike_AFFX-r2-Bs-dap_M_signal124.457100
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.968884
Spike_AFFX-r2-Ec-bioB_avg-signal12.469067
Spike_AFFX-r2-Bs-thr_avg-signal43.365772
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal569.924744
Spike_AFFX-r2-Bs-phe_5_signal18.313326
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal796.655579
RawQ2.944273
Spike_AFFX-r2-Bs-lys_5_signal14.201484
Signal(A)3.188131
%A28.391056
Signal(All)131.617233
Corner+Avg:171,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal177.792572
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal51.157127
Spike_AFFX-r2-Ec-bioD_avg-signal683.290161
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.153442
Spike_AFFX-r2-Bs-lys_avg-signal22.474062
Spike_AFFX-r2-P1-cre_avg-signal2800.614746
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.455502
Spike_AFFX-r2-Bs-thr_3_signal96.692802
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-signal30.481665
Spike_AFFX-r2-Bs-dap_3_signal274.104462
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.397826
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal176.724518
#M332
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.206203
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.006044
Spike_AFFX-r2-Bs-thr_M_signal26.482510
Signal(P)186.067123
Spike_AFFX-r2-Bs-phe_3-5-ratio2.793437
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9869,Count:9
Spike_AFFX-r2-P1-cre_5_signal2527.568115
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6476
Signal(M)12.339947
BackgroundAvg:70.88,Std:0.86,Min:68.6,Max:72.9
Spike_AFFX-r2-Ec-bioC_avg-signal177.258545
Spike_AFFX-r2-Bs-dap_avg-signal143.138306
Spike_AFFX-r2-Bs-dap_3-5-ratio8.884106
Spike_AFFX-r2-Ec-bioB_5_signal14.207231
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.347855
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-31_Col-0_Flowers_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 ("Quint_624-31_Col-0_Flowers_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: Quint_624-31_Col-0_Flowers_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.300609
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-ratio1.158098
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.818857
Spike_AFFX-r2-Bs-dap_5_signal30.987507
NoiseAvg:4.03,Std:0.13,Min:3.6,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.146621
#P16027
Spike_AFFX-r2-Bs-phe_M_signal24.831444
Corner-Avg:13857,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal21.424780
Spike_AFFX-r2-Ec-bioB_3_signal11.891392
Spike_AFFX-r2-Bs-lys_M_signal11.960367
Spike_AFFX-r2-P1-cre_3_signal2785.618408
Spike_AFFX-r2-Bs-lys_3-5-ratio2.147378
Spike_AFFX-r2-Bs-dap_M_signal147.226929
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.742463
Spike_AFFX-r2-Ec-bioB_avg-signal15.946038
Spike_AFFX-r2-Bs-thr_avg-signal38.093063
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal597.738098
Spike_AFFX-r2-Bs-phe_5_signal24.882101
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal858.870605
RawQ3.039447
Spike_AFFX-r2-Bs-lys_5_signal16.211147
Signal(A)3.251522
%A28.307760
Signal(All)130.668427
Corner+Avg:251,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal159.809525
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.924828
Spike_AFFX-r2-Ec-bioD_avg-signal728.304321
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.263046
Spike_AFFX-r2-Bs-lys_avg-signal20.994326
Spike_AFFX-r2-P1-cre_avg-signal2595.478516
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.429198
Spike_AFFX-r2-Bs-thr_3_signal83.918938
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-signal27.879457
Spike_AFFX-r2-Bs-dap_3_signal280.614258
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.436868
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal168.897888
#M326
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.811462
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.946190
Spike_AFFX-r2-Bs-thr_M_signal23.213627
Signal(P)184.407181
Spike_AFFX-r2-Bs-phe_3-5-ratio1.363423
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11364,Count:9
Spike_AFFX-r2-P1-cre_5_signal2405.338623
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6457
Signal(M)12.447123
BackgroundAvg:79.55,Std:1.29,Min:76.3,Max:82.7
Spike_AFFX-r2-Ec-bioC_avg-signal164.353699
Spike_AFFX-r2-Bs-dap_avg-signal152.942902
Spike_AFFX-r2-Bs-dap_3-5-ratio9.055722
Spike_AFFX-r2-Ec-bioB_5_signal14.521945
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.300609
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-32_Col-0_Flowers_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 ("Quint_624-32_Col-0_Flowers_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: Quint_624-32_Col-0_Flowers_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.357142
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-ratio1.160332
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.884297
Spike_AFFX-r2-Bs-dap_5_signal22.498978
NoiseAvg:3.83,Std:0.08,Min:3.6,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_signal3.365641
#P15766
Spike_AFFX-r2-Bs-phe_M_signal18.622793
Corner-Avg:11066,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal15.137360
Spike_AFFX-r2-Ec-bioB_3_signal12.693677
Spike_AFFX-r2-Bs-lys_M_signal11.694124
Spike_AFFX-r2-P1-cre_3_signal2842.170654
Spike_AFFX-r2-Bs-lys_3-5-ratio2.626006
Spike_AFFX-r2-Bs-dap_M_signal80.961838
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.676277
Spike_AFFX-r2-Ec-bioB_avg-signal14.061858
Spike_AFFX-r2-Bs-thr_avg-signal27.736589
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal608.390503
Spike_AFFX-r2-Bs-phe_5_signal15.171133
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal876.613403
RawQ3.087314
Spike_AFFX-r2-Bs-lys_5_signal10.103809
Signal(A)3.690818
%A29.263481
Signal(All)131.353928
Corner+Avg:207,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal173.171783
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.962593
Spike_AFFX-r2-Ec-bioD_avg-signal742.501953
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.118805
Spike_AFFX-r2-Bs-lys_avg-signal16.110201
Spike_AFFX-r2-P1-cre_avg-signal2645.808350
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.617712
Spike_AFFX-r2-Bs-thr_3_signal59.492001
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-signal20.252174
Spike_AFFX-r2-Bs-dap_3_signal188.266449
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.440873
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.473434
#M369
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.532667
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.954254
Spike_AFFX-r2-Bs-thr_M_signal20.352131
Signal(P)188.156876
Spike_AFFX-r2-Bs-phe_3-5-ratio1.777230
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9272,Count:9
Spike_AFFX-r2-P1-cre_5_signal2449.446045
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6675
Signal(M)13.727968
BackgroundAvg:75.94,Std:0.66,Min:72.9,Max:77.2
Spike_AFFX-r2-Ec-bioC_avg-signal177.322601
Spike_AFFX-r2-Bs-dap_avg-signal97.242409
Spike_AFFX-r2-Bs-dap_3-5-ratio8.367778
Spike_AFFX-r2-Ec-bioB_5_signal14.354537
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.357142
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-33_Col-0_Flowers_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 ("Quint_624-33_Col-0_Flowers_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: Quint_624-33_Col-0_Flowers_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::AT3G59940
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in AT3G59940
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.428324
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-ratio1.247279
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.813014
Spike_AFFX-r2-Bs-dap_5_signal29.122210
NoiseAvg:3.47,Std:0.09,Min:3.3,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_signal5.684983
#P15750
Spike_AFFX-r2-Bs-phe_M_signal22.988857
Corner-Avg:9880,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.492709
Spike_AFFX-r2-Ec-bioB_3_signal14.161808
Spike_AFFX-r2-Bs-lys_M_signal11.083009
Spike_AFFX-r2-P1-cre_3_signal3196.362061
Spike_AFFX-r2-Bs-lys_3-5-ratio2.329684
Spike_AFFX-r2-Bs-dap_M_signal110.524658
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.638577
Spike_AFFX-r2-Ec-bioB_avg-signal14.024470
Spike_AFFX-r2-Bs-thr_avg-signal37.233814
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal602.234985
Spike_AFFX-r2-Bs-phe_5_signal13.820818
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal814.985657
RawQ2.927412
Spike_AFFX-r2-Bs-lys_5_signal13.086212
Signal(A)3.688745
%A29.351162
Signal(All)131.616653
Corner+Avg:160,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.132813
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal37.501751
Spike_AFFX-r2-Ec-bioD_avg-signal708.610352
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.048660
Spike_AFFX-r2-Bs-lys_avg-signal18.218657
Spike_AFFX-r2-P1-cre_avg-signal2879.515625
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal83.220062
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-signal24.770475
Spike_AFFX-r2-Bs-dap_3_signal230.246704
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.353269
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal162.700775
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.486746
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.971924
Spike_AFFX-r2-Bs-thr_M_signal22.796396
Signal(P)188.736771
Spike_AFFX-r2-Bs-phe_3-5-ratio2.713425
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8639,Count:9
Spike_AFFX-r2-P1-cre_5_signal2562.668945
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6695
Signal(M)13.357552
BackgroundAvg:73.23,Std:1.13,Min:70.4,Max:76.1
Spike_AFFX-r2-Ec-bioC_avg-signal160.416794
Spike_AFFX-r2-Bs-dap_avg-signal123.297859
Spike_AFFX-r2-Bs-dap_3-5-ratio7.906224
Spike_AFFX-r2-Ec-bioB_5_signal17.418892
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.428324
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-34_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_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 ("Quint_624-34_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_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: Quint_624-34_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: AT1G15670-1/AT1G80440-1/AT3G59940-1
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G15670,AT1G80440,AT3G59940
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.383251
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-ratio1.181468
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.160304
Spike_AFFX-r2-Bs-dap_5_signal36.967186
NoiseAvg:3.25,Std:0.09,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_signal7.022713
#P15931
Spike_AFFX-r2-Bs-phe_M_signal29.281532
Corner-Avg:11825,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal13.324307
Spike_AFFX-r2-Ec-bioB_3_signal15.002458
Spike_AFFX-r2-Bs-lys_M_signal14.654898
Spike_AFFX-r2-P1-cre_3_signal3378.065186
Spike_AFFX-r2-Bs-lys_3-5-ratio1.927186
Spike_AFFX-r2-Bs-dap_M_signal169.180405
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.202781
Spike_AFFX-r2-Ec-bioB_avg-signal13.752177
Spike_AFFX-r2-Bs-thr_avg-signal41.476292
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal766.503235
Spike_AFFX-r2-Bs-phe_5_signal19.998148
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal997.368164
RawQ2.846488
Spike_AFFX-r2-Bs-lys_5_signal19.630688
Signal(A)3.004213
%A28.790005
Signal(All)133.122604
Corner+Avg:197,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal180.965317
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal48.629337
Spike_AFFX-r2-Ec-bioD_avg-signal881.935669
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.842171
Spike_AFFX-r2-Bs-lys_avg-signal24.039190
Spike_AFFX-r2-P1-cre_avg-signal3118.637695
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.367821
Spike_AFFX-r2-Bs-thr_3_signal85.696625
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-signal32.636341
Spike_AFFX-r2-Bs-dap_3_signal338.245178
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.301192
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal184.061920
#M312
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.831978
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.983176
Spike_AFFX-r2-Bs-thr_M_signal31.709541
Signal(P)189.130341
Spike_AFFX-r2-Bs-phe_3-5-ratio2.431692
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9148,Count:9
Spike_AFFX-r2-P1-cre_5_signal2859.210205
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6567
Signal(M)12.059415
BackgroundAvg:72.39,Std:0.79,Min:70.9,Max:74.4
Spike_AFFX-r2-Ec-bioC_avg-signal182.513611
Spike_AFFX-r2-Bs-dap_avg-signal181.464249
Spike_AFFX-r2-Bs-dap_3-5-ratio9.149877
Spike_AFFX-r2-Ec-bioB_5_signal12.929765
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.383251
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-35_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_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 ("Quint_624-35_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_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: Quint_624-35_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: AT1G15670-1/AT1G80440-1/AT3G59940-1
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G15670,AT1G80440,AT3G59940
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.350327
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-ratio1.194237
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.481797
Spike_AFFX-r2-Bs-dap_5_signal24.876942
NoiseAvg:3.51,Std:0.12,Min:3.3,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_signal4.128196
#P15878
Spike_AFFX-r2-Bs-phe_M_signal22.100056
Corner-Avg:12052,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal11.797860
Spike_AFFX-r2-Ec-bioB_3_signal10.772336
Spike_AFFX-r2-Bs-lys_M_signal19.518513
Spike_AFFX-r2-P1-cre_3_signal3024.900879
Spike_AFFX-r2-Bs-lys_3-5-ratio1.989233
Spike_AFFX-r2-Bs-dap_M_signal118.595497
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.086973
Spike_AFFX-r2-Ec-bioB_avg-signal9.946659
Spike_AFFX-r2-Bs-thr_avg-signal27.022001
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal713.022888
Spike_AFFX-r2-Bs-phe_5_signal15.076338
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal882.188477
RawQ2.907594
Spike_AFFX-r2-Bs-lys_5_signal12.519564
Signal(A)3.010198
%A28.833845
Signal(All)132.575745
Corner+Avg:209,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal164.473679
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal38.872467
Spike_AFFX-r2-Ec-bioD_avg-signal797.605713
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.609818
Spike_AFFX-r2-Bs-lys_avg-signal18.980803
Spike_AFFX-r2-P1-cre_avg-signal2778.907715
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.556335
Spike_AFFX-r2-Bs-thr_3_signal58.153782
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-signal25.349619
Spike_AFFX-r2-Bs-dap_3_signal242.299881
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.237251
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal159.074417
#M355
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.904331
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.033942
Spike_AFFX-r2-Bs-thr_M_signal18.784025
Signal(P)188.935471
Spike_AFFX-r2-Bs-phe_3-5-ratio2.578376
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9731,Count:9
Spike_AFFX-r2-P1-cre_5_signal2532.914795
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6577
Signal(M)12.217095
BackgroundAvg:75.57,Std:0.62,Min:73.9,Max:77.0
Spike_AFFX-r2-Ec-bioC_avg-signal161.774048
Spike_AFFX-r2-Bs-dap_avg-signal128.590775
Spike_AFFX-r2-Bs-dap_3-5-ratio9.739939
Spike_AFFX-r2-Ec-bioB_5_signal7.269780
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.350327
NF1.000000
HZ4
Tau0.015000

Slide: Quint_624-36_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_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 ("Quint_624-36_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_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: Quint_624-36_AT1G15670-1/AT1G80440-1/AT3G59940-1-Flowers_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: AT1G15670-1/AT1G80440-1/AT3G59940-1
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 2d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 5 min in 70 % Ethanol, 8 min in bleach followed by washing 3 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990). After 12 days on plates seedlings were transfered into plant pots (soil type GS90, mixed in ratio 4:3 with vermiculit) and cultivated in long day (16/8 light/dark) conditions.
Soil Constituentssoil type GS90, mixed in ratio 4:3 with vermiculit
Substrate Sterilising Procedureautoclaving
Temperature20 °C average, 20 °C day, 20 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G15670,AT1G80440,AT3G59940
Tissue: open flowers
Additional Organism Information:
Sample Description45 day old plants
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:0.35577
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-ratio1.294447
Spike_AFFX-r2-Ec-bioB_3-5-ratio5.935429
Spike_AFFX-r2-Bs-dap_5_signal19.969894
NoiseAvg:3.37,Std:0.09,Min:3.0,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.993856
#P15874
Spike_AFFX-r2-Bs-phe_M_signal22.364866
Corner-Avg:11304,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.557600
Spike_AFFX-r2-Ec-bioB_3_signal10.800763
Spike_AFFX-r2-Bs-lys_M_signal13.072874
Spike_AFFX-r2-P1-cre_3_signal3225.107422
Spike_AFFX-r2-Bs-lys_3-5-ratio3.729138
Spike_AFFX-r2-Bs-dap_M_signal100.106621
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio16.875324
Spike_AFFX-r2-Ec-bioB_avg-signal6.392691
Spike_AFFX-r2-Bs-thr_avg-signal31.317636
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal664.508423
Spike_AFFX-r2-Bs-phe_5_signal13.110242
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal780.103271
RawQ2.760629
Spike_AFFX-r2-Bs-lys_5_signal12.096237
Signal(A)3.102512
%A28.952213
Signal(All)134.471237
Corner+Avg:279,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal153.245712
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.069984
Spike_AFFX-r2-Ec-bioD_avg-signal722.305847
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.592285
Spike_AFFX-r2-Bs-lys_avg-signal23.425882
Spike_AFFX-r2-P1-cre_avg-signal2858.300537
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.455502
Spike_AFFX-r2-Bs-thr_3_signal67.397614
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-signal23.848366
Spike_AFFX-r2-Bs-dap_3_signal257.020966
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.173955
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal145.883926
#M332
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.108540
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.050463
Spike_AFFX-r2-Bs-thr_M_signal22.561441
Signal(P)191.674667
Spike_AFFX-r2-Bs-phe_3-5-ratio2.751283
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8953,Count:9
Spike_AFFX-r2-P1-cre_5_signal2491.493652
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6604
Signal(M)12.519006
BackgroundAvg:66.70,Std:0.47,Min:65.5,Max:68.1
Spike_AFFX-r2-Ec-bioC_avg-signal149.564819
Spike_AFFX-r2-Bs-dap_avg-signal125.699158
Spike_AFFX-r2-Bs-dap_3-5-ratio12.870421
Spike_AFFX-r2-Ec-bioB_5_signal1.819711
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.355770
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team