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Experiment: Identification of brg11 targets

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-618

The aim is to identify genes that are transcriptionally upregulated by Brg11 and related proteins. We use transgenic plants in which Brg11 and related proteins are induced by Estradiol. Thus we will have to compare a) Columbia without Estradiol application b) Columbia with Estradiol and c) Brg11 and related proteins under the control of the estradiol-inducible promoter.

About the Experimenter

Name:Dr. Thomas Lahaye
Head of Lab Name:Dr Thomas Lahaye
Lab:
Address:Institute for Genetics
Weinbergweg 10
Halle (Saale)
Postcode: 06120
Country: Germany
 
Telephone Number: 00493455526345

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

About this Experiment

Experiment Type: compound_based_treatment; strain_or_line_design;
Number of Slides:5
 
Experimental Parameters:
parameter compound_based_treatment
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Lahaye: Identification of brg11 targets

Slide: Lahaye_618-1_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 ("Lahaye_618-1_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: Lahaye_618-1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-transgenic with Avr3*
Stock Code:
Genetic Background: Col
Growth Conditions:
Sample descriptionCol-transgenic with Avr3* under Estradiol-inducible promoter; treated with Estradiol
Tissue: Whole plant
in vivo Treatment:
TreatmentTreated with Estradiol
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:0.618279
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-ratio1.324358
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.290926
Spike_AFFX-r2-Bs-dap_5_signal192.259476
NoiseAvg:2.20,Std:0.03,Min:2.1,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal27.050545
#P13900
Spike_AFFX-r2-Bs-phe_M_signal210.538330
Corner-Avg:15485,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal149.253525
Spike_AFFX-r2-Ec-bioB_3_signal140.171753
Spike_AFFX-r2-Bs-lys_M_signal148.632706
Spike_AFFX-r2-P1-cre_3_signal6433.129395
Spike_AFFX-r2-Bs-lys_3-5-ratio1.866821
Spike_AFFX-r2-Bs-dap_M_signal1048.785278
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio33.586452
Spike_AFFX-r2-Ec-bioB_avg-signal132.669220
Spike_AFFX-r2-Bs-thr_avg-signal405.152008
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1349.332397
Spike_AFFX-r2-Bs-phe_5_signal177.119598
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2101.185791
RawQ2.054257
Spike_AFFX-r2-Bs-lys_5_signal113.772736
Signal(A)3.057881
%A37.645771
Signal(All)144.918594
Corner+Avg:124,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal435.489044
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal520.671875
Spike_AFFX-r2-Ec-bioD_avg-signal1725.259033
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.938187
Spike_AFFX-r2-Bs-lys_avg-signal158.266251
Spike_AFFX-r2-P1-cre_avg-signal5645.336914
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.416046
Spike_AFFX-r2-Bs-thr_3_signal908.531860
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-signal302.776611
Spike_AFFX-r2-Bs-dap_3_signal1894.316162
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.557204
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal426.092072
#M323
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal212.393280
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.022054
Spike_AFFX-r2-Bs-thr_M_signal279.873718
Signal(P)235.633987
Spike_AFFX-r2-Bs-phe_3-5-ratio2.939663
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12664,Count:9
Spike_AFFX-r2-P1-cre_5_signal4857.544434
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8587
Signal(M)12.454267
BackgroundAvg:49.72,Std:0.35,Min:48.7,Max:50.6
Spike_AFFX-r2-Ec-bioC_avg-signal430.790558
Spike_AFFX-r2-Bs-dap_avg-signal1045.120361
Spike_AFFX-r2-Bs-dap_3-5-ratio9.852915
Spike_AFFX-r2-Ec-bioB_5_signal108.582359
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.618279
NF1.000000
HZ4
Tau0.015000

Slide: Lahaye_618-2_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 ("Lahaye_618-2_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: Lahaye_618-2_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-transgenic with Brg11*
Stock Code:
Genetic Background: Col
Growth Conditions:
Sample descriptionCol-transgenic with Brg11* under Estradiol-inducible promoter; treated with Estradiol
Tissue: Whole plant
in vivo Treatment:
TreatmentTreated with Estradiol
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:0.619576
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-ratio1.323503
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.555816
Spike_AFFX-r2-Bs-dap_5_signal293.101715
NoiseAvg:2.56,Std:0.10,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal68.534164
#P13679
Spike_AFFX-r2-Bs-phe_M_signal183.887390
Corner-Avg:14969,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal98.761696
Spike_AFFX-r2-Ec-bioB_3_signal100.983917
Spike_AFFX-r2-Bs-lys_M_signal79.626724
Spike_AFFX-r2-P1-cre_3_signal5131.728516
Spike_AFFX-r2-Bs-lys_3-5-ratio1.481005
Spike_AFFX-r2-Bs-dap_M_signal847.912842
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.643852
Spike_AFFX-r2-Ec-bioB_avg-signal88.217651
Spike_AFFX-r2-Bs-thr_avg-signal345.117523
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal968.577637
Spike_AFFX-r2-Bs-phe_5_signal158.072937
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1557.736572
RawQ2.288569
Spike_AFFX-r2-Bs-lys_5_signal88.739235
Signal(A)3.647985
%A38.404209
Signal(All)144.022324
Corner+Avg:122,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal323.816895
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal405.719666
Spike_AFFX-r2-Ec-bioD_avg-signal1263.157104
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.969311
Spike_AFFX-r2-Bs-lys_avg-signal99.929749
Spike_AFFX-r2-P1-cre_avg-signal4504.555664
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_signal660.933350
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-signal249.226669
Spike_AFFX-r2-Bs-dap_3_signal1265.071777
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.608272
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal303.819916
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal131.423294
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.065819
Spike_AFFX-r2-Bs-thr_M_signal305.885071
Signal(P)237.456009
Spike_AFFX-r2-Bs-phe_3-5-ratio2.566661
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11808,Count:9
Spike_AFFX-r2-P1-cre_5_signal3877.382568
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8760
Signal(M)13.563628
BackgroundAvg:54.63,Std:0.38,Min:53.7,Max:56.0
Spike_AFFX-r2-Ec-bioC_avg-signal313.818420
Spike_AFFX-r2-Bs-dap_avg-signal802.028809
Spike_AFFX-r2-Bs-dap_3-5-ratio4.316153
Spike_AFFX-r2-Ec-bioB_5_signal64.907364
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.619576
NF1.000000
HZ4
Tau0.015000

Slide: Lahaye_618-3_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 ("Lahaye_618-3_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Lahaye_618-3_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-transgenic with Avr4*
Stock Code:
Genetic Background: Col
Growth Conditions:
Sample descriptionCol-transgenic with Avr4* under Estradiol-inducible promoter; treated with Estradiol
Tissue: Whole plant
in vivo Treatment:
TreatmentTreated with Estradiol
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:0.676873
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-ratio1.375842
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.724166
Spike_AFFX-r2-Bs-dap_5_signal236.959641
NoiseAvg:2.68,Std:0.05,Min:2.6,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal61.122112
#P13510
Spike_AFFX-r2-Bs-phe_M_signal170.585938
Corner-Avg:15230,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal121.667374
Spike_AFFX-r2-Ec-bioB_3_signal116.101898
Spike_AFFX-r2-Bs-lys_M_signal68.219589
Spike_AFFX-r2-P1-cre_3_signal5946.895508
Spike_AFFX-r2-Bs-lys_3-5-ratio1.375731
Spike_AFFX-r2-Bs-dap_M_signal764.361816
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.473838
Spike_AFFX-r2-Ec-bioB_avg-signal101.702423
Spike_AFFX-r2-Bs-thr_avg-signal302.785034
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1096.484863
Spike_AFFX-r2-Bs-phe_5_signal132.850082
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1825.021240
RawQ2.413285
Spike_AFFX-r2-Bs-lys_5_signal82.218475
Signal(A)4.351621
%A39.162647
Signal(All)152.523911
Corner+Avg:127,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal370.100372
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal391.928802
Spike_AFFX-r2-Ec-bioD_avg-signal1460.753052
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.228409
Spike_AFFX-r2-Bs-lys_avg-signal87.849525
Spike_AFFX-r2-P1-cre_avg-signal5134.631836
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal579.060974
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-signal231.788284
Spike_AFFX-r2-Bs-dap_3_signal1203.082764
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.664429
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal342.360779
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal113.110504
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.081024
Spike_AFFX-r2-Bs-thr_M_signal268.171997
Signal(P)254.152893
Spike_AFFX-r2-Bs-phe_3-5-ratio2.950159
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11344,Count:9
Spike_AFFX-r2-P1-cre_5_signal4322.368652
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8933
Signal(M)17.961344
BackgroundAvg:59.53,Std:0.62,Min:58.2,Max:61.4
Spike_AFFX-r2-Ec-bioC_avg-signal356.230591
Spike_AFFX-r2-Bs-dap_avg-signal734.801453
Spike_AFFX-r2-Bs-dap_3-5-ratio5.077163
Spike_AFFX-r2-Ec-bioB_5_signal67.337990
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.676873
NF1.000000
HZ4
Tau0.015000

Slide: Lahaye_618-4_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 ("Lahaye_618-4_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: Lahaye_618-4_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-WT
Stock Code:
Growth Conditions:
Sample descriptionCol-WT; treated with Estradiol
Tissue: Whole plant
in vivo Treatment:
TreatmentTreated with Estradiol
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:0.597198
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-ratio1.268660
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.244998
Spike_AFFX-r2-Bs-dap_5_signal219.235367
NoiseAvg:2.60,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal43.099514
#P13539
Spike_AFFX-r2-Bs-phe_M_signal143.739822
Corner-Avg:14164,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal104.004623
Spike_AFFX-r2-Ec-bioB_3_signal98.058319
Spike_AFFX-r2-Bs-lys_M_signal73.886513
Spike_AFFX-r2-P1-cre_3_signal5261.461914
Spike_AFFX-r2-Bs-lys_3-5-ratio1.624497
Spike_AFFX-r2-Bs-dap_M_signal662.161926
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.533030
Spike_AFFX-r2-Ec-bioB_avg-signal93.608269
Spike_AFFX-r2-Bs-thr_avg-signal268.703522
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1065.738159
Spike_AFFX-r2-Bs-phe_5_signal137.707108
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1528.312134
RawQ2.449197
Spike_AFFX-r2-Bs-lys_5_signal68.648384
Signal(A)3.602230
%A39.053047
Signal(All)146.013901
Corner+Avg:114,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal324.323242
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal278.388794
Spike_AFFX-r2-Ec-bioD_avg-signal1297.025146
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.355545
Spike_AFFX-r2-Bs-lys_avg-signal84.684654
Spike_AFFX-r2-P1-cre_avg-signal4704.360352
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal540.167480
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-signal186.611893
Spike_AFFX-r2-Bs-dap_3_signal1175.120605
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.434041
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal315.837677
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal111.519066
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.026867
Spike_AFFX-r2-Bs-thr_M_signal222.843597
Signal(P)243.250275
Spike_AFFX-r2-Bs-phe_3-5-ratio2.021601
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11842,Count:9
Spike_AFFX-r2-P1-cre_5_signal4147.258789
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8908
Signal(M)14.112928
BackgroundAvg:60.13,Std:0.56,Min:58.3,Max:61.1
Spike_AFFX-r2-Ec-bioC_avg-signal320.080444
Spike_AFFX-r2-Bs-dap_avg-signal685.505920
Spike_AFFX-r2-Bs-dap_3-5-ratio5.360087
Spike_AFFX-r2-Ec-bioB_5_signal78.761848
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.597198
NF1.000000
HZ4
Tau0.015000

Slide: Lahaye_618-5_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 ("Lahaye_618-5_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: Lahaye_618-5_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Pooled Col-transgenic with Avr3*, Avr4*, Brg11
Stock Code:
Genetic Background: Col
Growth Conditions:
Sample descriptionPooled material of Col-transgenic with Avr3* / Avr4* / Brg11*; non-treated
Tissue: Whole plant
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:0.631821
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-ratio1.212824
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.852192
Spike_AFFX-r2-Bs-dap_5_signal269.318573
NoiseAvg:2.62,Std:0.10,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal69.814934
#P13832
Spike_AFFX-r2-Bs-phe_M_signal171.205185
Corner-Avg:16568,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.962914
Spike_AFFX-r2-Ec-bioB_3_signal93.139977
Spike_AFFX-r2-Bs-lys_M_signal78.031425
Spike_AFFX-r2-P1-cre_3_signal5185.000000
Spike_AFFX-r2-Bs-lys_3-5-ratio1.993237
Spike_AFFX-r2-Bs-dap_M_signal846.123291
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.513122
Spike_AFFX-r2-Ec-bioB_avg-signal80.129753
Spike_AFFX-r2-Bs-thr_avg-signal377.481689
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal970.511841
Spike_AFFX-r2-Bs-phe_5_signal143.733521
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1672.126587
RawQ2.360414
Spike_AFFX-r2-Bs-lys_5_signal77.424026
Signal(A)4.124879
%A37.799210
Signal(All)143.780258
Corner+Avg:125,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal340.998657
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal377.636688
Spike_AFFX-r2-Ec-bioD_avg-signal1321.319214
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.640072
Spike_AFFX-r2-Bs-lys_avg-signal103.259972
Spike_AFFX-r2-P1-cre_avg-signal4730.073242
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.560719
Spike_AFFX-r2-Bs-thr_3_signal733.972900
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-signal230.858459
Spike_AFFX-r2-Bs-dap_3_signal1410.749512
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.722933
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal313.492920
#M356
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal154.324448
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.087740
Spike_AFFX-r2-Bs-thr_M_signal328.657166
Signal(P)234.112473
Spike_AFFX-r2-Bs-phe_3-5-ratio2.627339
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13106,Count:9
Spike_AFFX-r2-P1-cre_5_signal4275.146973
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8622
Signal(M)16.346148
BackgroundAvg:59.34,Std:0.58,Min:57.3,Max:60.8
Spike_AFFX-r2-Ec-bioC_avg-signal327.245789
Spike_AFFX-r2-Bs-dap_avg-signal842.063782
Spike_AFFX-r2-Bs-dap_3-5-ratio5.238218
Spike_AFFX-r2-Ec-bioB_5_signal50.286354
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.631821
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team