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Experiment: Crosstalk between the defense hormones salicylic acid (SA) and jasmonic acid (JA).

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-684

Aims:

Elucidating genes affected by hormonal crosstalk between SA and JA in Arabidopsis thaliana.

Background:

5 week old Col-0 plants grown 8h day / 16h night cycle at 70% RH and 20 degrees Celsius.

Tissues:

All aboveground parts (whole rosette) of at least 5 plants per treatment were harvested for RNA extraction.

Treatment:

To all treatments 0.015% v/v silwet was added.Mock (Water), 1 mM SA, 0.1 mM MeJA or 1 mM SA + 0.1 mM MeJA

Each treatment was performed on 3 independent biological replicates.

Paper:

Van der Does et al. (2013) The Plant Cell

About the Experimenter

Name:Prof. Dr. Corne Pieterse
Head of Lab Name:Prof. Dr. Corne Pieterse
Lab:
Address:Utrecht University
Plant-Microbe Interactions
Padualaan 8
Postcode: 3584 CH Utrecht
Country: The Netherlands
 

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:12
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Pieterse: Crosstalk between the defense hormones salicylic acid (SA) and jasmonic acid (JA).

Slide: Pieterse_6241-1_Mock-treated_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 ("Pieterse_6241-1_Mock-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-1_Mock-treated_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet
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:2.489904
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-ratio1.780038
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.516257
Spike_AFFX-r2-Bs-dap_5_signal49.844582
NoiseAvg:1.98,Std:0.27,Min:1.7,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal3.374638
#P11813
Spike_AFFX-r2-Bs-phe_M_signal9.112314
Corner-Avg:371,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.381845
Spike_AFFX-r2-Ec-bioB_3_signal11.043078
Spike_AFFX-r2-Bs-lys_M_signal16.745619
Spike_AFFX-r2-P1-cre_3_signal243.555283
Spike_AFFX-r2-Bs-lys_3-5-ratio0.856170
Spike_AFFX-r2-Bs-dap_M_signal56.652500
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.061028
Spike_AFFX-r2-Ec-bioB_avg-signal14.271866
Spike_AFFX-r2-Bs-thr_avg-signal20.919741
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal13.981368
Spike_AFFX-r2-Bs-phe_5_signal20.072651
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal27.551826
RawQ1.886225
Spike_AFFX-r2-Bs-lys_5_signal11.601536
Signal(A)12.586247
%A45.734325
Signal(All)151.527939
Corner+Avg:16,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionA
Spike_AFFX-r2-Ec-bioC_3_signal26.040169
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal12.950061
Spike_AFFX-r2-Ec-bioD_avg-signal20.766598
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P51.788689
Spike_AFFX-r2-Bs-lys_avg-signal12.760015
Spike_AFFX-r2-P1-cre_avg-signal190.190598
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.476984
Spike_AFFX-r2-Bs-thr_3_signal20.453779
Spike_AFFX-r2-Ec-bioC_5_detectionA
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal14.045009
Spike_AFFX-r2-Bs-dap_3_signal76.875481
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.970610
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal7.598461
#M565
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal9.932892
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio3.427032
Spike_AFFX-r2-Bs-thr_M_signal38.930805
Signal(P)279.592102
Spike_AFFX-r2-Bs-phe_3-5-ratio0.645159
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:331,Count:9
Spike_AFFX-r2-P1-cre_5_signal136.825912
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10432
Signal(M)39.347031
BackgroundAvg:50.62,Std:1.47,Min:46.9,Max:55.8
Spike_AFFX-r2-Ec-bioC_avg-signal16.819315
Spike_AFFX-r2-Bs-dap_avg-signal61.124187
Spike_AFFX-r2-Bs-dap_3-5-ratio1.542304
Spike_AFFX-r2-Ec-bioB_5_signal21.390675
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.489904
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-2_1mM-SA-treated_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 ("Pieterse_6241-2_1mM-SA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-2_1mM-SA-treated_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 1mM SA
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:2.104866
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-ratio1.452145
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.348078
Spike_AFFX-r2-Bs-dap_5_signal27.233042
NoiseAvg:2.07,Std:0.10,Min:1.9,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal13.235799
#P12119
Spike_AFFX-r2-Bs-phe_M_signal1.921986
Corner-Avg:371,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal7.153294
Spike_AFFX-r2-Ec-bioB_3_signal10.133252
Spike_AFFX-r2-Bs-lys_M_signal0.720708
Spike_AFFX-r2-P1-cre_3_signal189.998840
Spike_AFFX-r2-Bs-lys_3-5-ratio1.935741
Spike_AFFX-r2-Bs-dap_M_signal35.158195
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.455029
Spike_AFFX-r2-Ec-bioB_avg-signal8.267787
Spike_AFFX-r2-Bs-thr_avg-signal15.620235
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal14.195026
Spike_AFFX-r2-Bs-phe_5_signal1.857283
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal21.312761
RawQ2.007645
Spike_AFFX-r2-Bs-lys_5_signal12.716083
Signal(A)11.977515
%A44.454185
Signal(All)147.725662
Corner+Avg:15,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionA
Spike_AFFX-r2-Ec-bioC_3_signal20.250492
Spike_AFFX-r2-Bs-lys_3_detectionM
Spike_AFFX-r2-Bs-phe_3_signal21.270376
Spike_AFFX-r2-Ec-bioD_avg-signal17.753895
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P53.130207
Spike_AFFX-r2-Bs-lys_avg-signal12.683944
Spike_AFFX-r2-P1-cre_avg-signal160.419495
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.415607
Spike_AFFX-r2-Bs-thr_3_signal6.022671
Spike_AFFX-r2-Ec-bioC_5_detectionA
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal8.349881
Spike_AFFX-r2-Bs-dap_3_signal43.893452
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.501425
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal11.573242
#M551
Spike_AFFX-r2-Bs-lys_5_detectionM
Spike_AFFX-r2-Bs-lys_3_signal24.615038
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.749768
Spike_AFFX-r2-Bs-thr_M_signal27.602238
Signal(P)266.390839
Spike_AFFX-r2-Bs-phe_3-5-ratio11.452416
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:378,Count:9
Spike_AFFX-r2-P1-cre_5_signal130.840164
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10140
Signal(M)35.897953
BackgroundAvg:51.48,Std:1.03,Min:49.4,Max:55.0
Spike_AFFX-r2-Ec-bioC_avg-signal15.911867
Spike_AFFX-r2-Bs-dap_avg-signal35.428230
Spike_AFFX-r2-Bs-dap_3-5-ratio1.611772
Spike_AFFX-r2-Ec-bioB_5_signal7.516814
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.104866
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-3_0.1mM-MeJA-treated_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 ("Pieterse_6241-3_0.1mM-MeJA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-3_0.1mM-MeJA-treated_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 0.1mM MeJA
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:2.259553
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-ratio1.073325
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.774443
Spike_AFFX-r2-Bs-dap_5_signal31.705433
NoiseAvg:2.36,Std:0.61,Min:1.6,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_signal29.784151
#P11555
Spike_AFFX-r2-Bs-phe_M_signal14.011167
Corner-Avg:5423,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal128.780472
Spike_AFFX-r2-Ec-bioB_3_signal101.634132
Spike_AFFX-r2-Bs-lys_M_signal16.498947
Spike_AFFX-r2-P1-cre_3_signal4925.393555
Spike_AFFX-r2-Bs-lys_3-5-ratio6.073978
Spike_AFFX-r2-Bs-dap_M_signal64.576302
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.069176
Spike_AFFX-r2-Ec-bioB_avg-signal120.549889
Spike_AFFX-r2-Bs-thr_avg-signal53.041306
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1143.104492
Spike_AFFX-r2-Bs-phe_5_signal3.560630
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1577.768799
RawQ1.939029
Spike_AFFX-r2-Bs-lys_5_signal4.908985
Signal(A)13.094753
%A46.896099
Signal(All)150.101364
Corner+Avg:57,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal426.438995
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal23.524714
Spike_AFFX-r2-Ec-bioD_avg-signal1360.436646
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P50.657608
Spike_AFFX-r2-Bs-lys_avg-signal17.074999
Spike_AFFX-r2-P1-cre_avg-signal4757.152344
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.446295
Spike_AFFX-r2-Bs-thr_3_signal61.628658
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal13.698837
Spike_AFFX-r2-Bs-dap_3_signal59.315979
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.380249
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal495.904999
#M558
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal29.817066
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.859921
Spike_AFFX-r2-Bs-thr_M_signal67.711113
Signal(P)282.129486
Spike_AFFX-r2-Bs-phe_3-5-ratio6.606897
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5426,Count:9
Spike_AFFX-r2-P1-cre_5_signal4588.911133
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10697
Signal(M)42.529030
BackgroundAvg:48.71,Std:4.32,Min:42.1,Max:62.3
Spike_AFFX-r2-Ec-bioC_avg-signal461.171997
Spike_AFFX-r2-Bs-dap_avg-signal51.865906
Spike_AFFX-r2-Bs-dap_3-5-ratio1.870846
Spike_AFFX-r2-Ec-bioB_5_signal131.235062
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.259553
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-4_1mM-SA-and-0.1-mM MeJA-treated_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 ("Pieterse_6241-4_1mM-SA-and-0.1-mM MeJA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-4_1mM-SA-and-0.1-mM MeJA-treated_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 1mM SA + 0.1mM MeJA
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:3.073547
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-ratio1.308567
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.770568
Spike_AFFX-r2-Bs-dap_5_signal41.258488
NoiseAvg:1.39,Std:0.07,Min:1.2,Max:1.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.165541
#P12893
Spike_AFFX-r2-Bs-phe_M_signal12.451795
Corner-Avg:4416,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal127.032455
Spike_AFFX-r2-Ec-bioB_3_signal138.228104
Spike_AFFX-r2-Bs-lys_M_signal1.791654
Spike_AFFX-r2-P1-cre_3_signal6160.904297
Spike_AFFX-r2-Bs-lys_3-5-ratio1.760899
Spike_AFFX-r2-Bs-dap_M_signal53.186298
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.192299
Spike_AFFX-r2-Ec-bioB_avg-signal148.215073
Spike_AFFX-r2-Bs-thr_avg-signal33.301926
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1317.323486
Spike_AFFX-r2-Bs-phe_5_signal15.626587
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1787.515137
RawQ1.557017
Spike_AFFX-r2-Bs-lys_5_signal4.320843
Signal(A)7.354139
%A41.565102
Signal(All)154.240585
Corner+Avg:31,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal531.941528
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal5.646495
Spike_AFFX-r2-Ec-bioD_avg-signal1552.419312
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.523453
Spike_AFFX-r2-Bs-lys_avg-signal4.573688
Spike_AFFX-r2-P1-cre_avg-signal5434.516602
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.911442
Spike_AFFX-r2-Bs-thr_3_signal37.158642
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal11.241626
Spike_AFFX-r2-Bs-dap_3_signal49.710365
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.356930
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal493.207275
#M436
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal7.608566
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.078535
Spike_AFFX-r2-Bs-thr_M_signal31.581594
Signal(P)266.603149
Spike_AFFX-r2-Bs-phe_3-5-ratio0.361339
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4430,Count:9
Spike_AFFX-r2-P1-cre_5_signal4708.129395
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9481
Signal(M)25.662415
BackgroundAvg:40.92,Std:0.63,Min:39.9,Max:42.8
Spike_AFFX-r2-Ec-bioC_avg-signal512.574402
Spike_AFFX-r2-Bs-dap_avg-signal48.051716
Spike_AFFX-r2-Bs-dap_3-5-ratio1.204852
Spike_AFFX-r2-Ec-bioB_5_signal179.384674
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF3.073547
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-5_Mock-treated_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 ("Pieterse_6241-5_Mock-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-5_Mock-treated_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet
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:1.384493
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-ratio1.414449
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.924293
Spike_AFFX-r2-Bs-dap_5_signal316.547882
NoiseAvg:2.12,Std:0.10,Min:1.9,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal133.323654
#P13657
Spike_AFFX-r2-Bs-phe_M_signal94.120201
Corner-Avg:10634,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal136.269684
Spike_AFFX-r2-Ec-bioB_3_signal107.718315
Spike_AFFX-r2-Bs-lys_M_signal48.608707
Spike_AFFX-r2-P1-cre_3_signal5521.775391
Spike_AFFX-r2-Bs-lys_3-5-ratio1.530881
Spike_AFFX-r2-Bs-dap_M_signal496.506622
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.943973
Spike_AFFX-r2-Ec-bioB_avg-signal120.176430
Spike_AFFX-r2-Bs-thr_avg-signal213.836777
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1129.916138
Spike_AFFX-r2-Bs-phe_5_signal94.313019
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1658.633667
RawQ2.092227
Spike_AFFX-r2-Bs-lys_5_signal51.677952
Signal(A)5.835657
%A38.149933
Signal(All)148.983597
Corner+Avg:96,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal411.941101
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal125.502197
Spike_AFFX-r2-Ec-bioD_avg-signal1394.274902
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.872864
Spike_AFFX-r2-Bs-lys_avg-signal59.799809
Spike_AFFX-r2-P1-cre_avg-signal4712.804688
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.977203
Spike_AFFX-r2-Bs-thr_3_signal259.177612
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-signal104.645142
Spike_AFFX-r2-Bs-dap_3_signal553.838684
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.467926
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal426.861664
#M451
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal79.112778
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.965046
Spike_AFFX-r2-Bs-thr_M_signal249.009018
Signal(P)244.412918
Spike_AFFX-r2-Bs-phe_3-5-ratio1.330698
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10374,Count:9
Spike_AFFX-r2-P1-cre_5_signal3903.834473
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8702
Signal(M)21.256245
BackgroundAvg:50.02,Std:1.28,Min:47.9,Max:53.2
Spike_AFFX-r2-Ec-bioC_avg-signal419.401367
Spike_AFFX-r2-Bs-dap_avg-signal455.631073
Spike_AFFX-r2-Bs-dap_3-5-ratio1.749621
Spike_AFFX-r2-Ec-bioB_5_signal116.541275
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.384493
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-6_1mM-SA-treated_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 ("Pieterse_6241-6_1mM-SA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-6_1mM-SA-treated_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 1mM SA
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:1.189238
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-ratio1.320071
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.805727
Spike_AFFX-r2-Bs-dap_5_signal227.617767
NoiseAvg:1.74,Std:0.05,Min:1.6,Max:1.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal128.007507
#P14337
Spike_AFFX-r2-Bs-phe_M_signal86.461243
Corner-Avg:9625,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal120.707550
Spike_AFFX-r2-Ec-bioB_3_signal93.130875
Spike_AFFX-r2-Bs-lys_M_signal37.627296
Spike_AFFX-r2-P1-cre_3_signal4569.729004
Spike_AFFX-r2-Bs-lys_3-5-ratio2.292294
Spike_AFFX-r2-Bs-dap_M_signal408.497009
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.763230
Spike_AFFX-r2-Ec-bioB_avg-signal109.808167
Spike_AFFX-r2-Bs-thr_avg-signal252.571716
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1065.029419
Spike_AFFX-r2-Bs-phe_5_signal110.888039
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1313.211548
RawQ1.774573
Spike_AFFX-r2-Bs-lys_5_signal47.337639
Signal(A)4.458976
%A35.567734
Signal(All)145.063309
Corner+Avg:87,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal346.899567
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal117.976250
Spike_AFFX-r2-Ec-bioD_avg-signal1189.120483
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.854012
Spike_AFFX-r2-Bs-lys_avg-signal64.492241
Spike_AFFX-r2-P1-cre_avg-signal4015.729248
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal353.714142
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-signal105.108513
Spike_AFFX-r2-Bs-dap_3_signal519.597778
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.233028
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal359.492401
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal108.511765
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.964971
Spike_AFFX-r2-Bs-thr_M_signal275.993469
Signal(P)227.850586
Spike_AFFX-r2-Bs-phe_3-5-ratio1.063922
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8093,Count:9
Spike_AFFX-r2-P1-cre_5_signal3461.729492
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8113
Signal(M)16.735353
BackgroundAvg:40.90,Std:0.75,Min:39.7,Max:44.0
Spike_AFFX-r2-Ec-bioC_avg-signal353.195984
Spike_AFFX-r2-Bs-dap_avg-signal385.237518
Spike_AFFX-r2-Bs-dap_3-5-ratio2.282765
Spike_AFFX-r2-Ec-bioB_5_signal115.586090
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.189238
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-7_0.1mM-MeJA-treated_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 ("Pieterse_6241-7_0.1mM-MeJA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-7_0.1mM-MeJA-treated_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 0.1mM MeJA
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:1.378509
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-ratio1.273379
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.849422
Spike_AFFX-r2-Bs-dap_5_signal208.725327
NoiseAvg:1.97,Std:0.08,Min:1.7,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_signal103.838676
#P13876
Spike_AFFX-r2-Bs-phe_M_signal95.349899
Corner-Avg:10380,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal136.629089
Spike_AFFX-r2-Ec-bioB_3_signal113.677773
Spike_AFFX-r2-Bs-lys_M_signal39.039761
Spike_AFFX-r2-P1-cre_3_signal5023.600586
Spike_AFFX-r2-Bs-lys_3-5-ratio1.086760
Spike_AFFX-r2-Bs-dap_M_signal361.275574
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.032954
Spike_AFFX-r2-Ec-bioB_avg-signal128.045486
Spike_AFFX-r2-Bs-thr_avg-signal216.555618
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1063.630859
Spike_AFFX-r2-Bs-phe_5_signal99.686615
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1505.676636
RawQ1.984885
Spike_AFFX-r2-Bs-lys_5_signal60.093964
Signal(A)5.106612
%A37.373959
Signal(All)147.667099
Corner+Avg:89,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal433.696198
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal99.614983
Spike_AFFX-r2-Ec-bioD_avg-signal1284.653809
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.832970
Spike_AFFX-r2-Bs-lys_avg-signal54.813816
Spike_AFFX-r2-P1-cre_avg-signal4484.346680
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.793073
Spike_AFFX-r2-Bs-thr_3_signal314.937988
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-signal98.217163
Spike_AFFX-r2-Bs-dap_3_signal414.672455
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.415601
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal443.048218
#M409
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal65.307732
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.978892
Spike_AFFX-r2-Bs-thr_M_signal230.890213
Signal(P)239.063690
Spike_AFFX-r2-Bs-phe_3-5-ratio0.999281
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10031,Count:9
Spike_AFFX-r2-P1-cre_5_signal3945.093262
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8525
Signal(M)18.349510
BackgroundAvg:45.55,Std:0.84,Min:42.9,Max:48.1
Spike_AFFX-r2-Ec-bioC_avg-signal438.372192
Spike_AFFX-r2-Bs-dap_avg-signal328.224457
Spike_AFFX-r2-Bs-dap_3-5-ratio1.986690
Spike_AFFX-r2-Ec-bioB_5_signal133.829590
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.378509
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-8_1mM-SA-and-0.1mM-MeJA treated_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 ("Pieterse_6241-8_1mM-SA-and-0.1mM-MeJA treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-8_1mM-SA-and-0.1mM-MeJA treated_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 1mM SA + 0.1mM MeJA
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:1.495946
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-ratio1.334961
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.048605
Spike_AFFX-r2-Bs-dap_5_signal207.367020
NoiseAvg:2.03,Std:0.17,Min:1.8,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_signal111.857719
#P13599
Spike_AFFX-r2-Bs-phe_M_signal56.088150
Corner-Avg:8751,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal112.294090
Spike_AFFX-r2-Ec-bioB_3_signal98.763168
Spike_AFFX-r2-Bs-lys_M_signal37.441216
Spike_AFFX-r2-P1-cre_3_signal4933.959961
Spike_AFFX-r2-Bs-lys_3-5-ratio0.828790
Spike_AFFX-r2-Bs-dap_M_signal329.537048
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.546088
Spike_AFFX-r2-Ec-bioB_avg-signal101.747498
Spike_AFFX-r2-Bs-thr_avg-signal208.132339
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1007.603149
Spike_AFFX-r2-Bs-phe_5_signal96.330681
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1341.906616
RawQ1.957015
Spike_AFFX-r2-Bs-lys_5_signal48.295338
Signal(A)6.028465
%A38.465584
Signal(All)147.565384
Corner+Avg:75,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal432.963593
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal112.811844
Spike_AFFX-r2-Ec-bioD_avg-signal1174.754883
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.618587
Spike_AFFX-r2-Bs-lys_avg-signal41.921082
Spike_AFFX-r2-P1-cre_avg-signal4314.958984
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.915826
Spike_AFFX-r2-Bs-thr_3_signal284.799622
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-signal88.410225
Spike_AFFX-r2-Bs-dap_3_signal328.876923
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.331781
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal352.227295
#M437
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.026699
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.229216
Spike_AFFX-r2-Bs-thr_M_signal227.739716
Signal(P)242.898453
Spike_AFFX-r2-Bs-phe_3-5-ratio1.171089
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9008,Count:9
Spike_AFFX-r2-P1-cre_5_signal3695.958252
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8774
Signal(M)22.646458
BackgroundAvg:45.50,Std:0.21,Min:44.9,Max:46.3
Spike_AFFX-r2-Ec-bioC_avg-signal392.595459
Spike_AFFX-r2-Bs-dap_avg-signal288.593658
Spike_AFFX-r2-Bs-dap_3-5-ratio1.585965
Spike_AFFX-r2-Ec-bioB_5_signal94.185257
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.495946
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-9_Mock-treated_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 ("Pieterse_6241-9_Mock-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-9_Mock-treated_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet
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:1.200134
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-ratio1.255900
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.741037
Spike_AFFX-r2-Bs-dap_5_signal201.029388
NoiseAvg:2.07,Std:0.05,Min:2.0,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal156.362152
#P14122
Spike_AFFX-r2-Bs-phe_M_signal76.533539
Corner-Avg:11555,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal115.909485
Spike_AFFX-r2-Ec-bioB_3_signal98.609756
Spike_AFFX-r2-Bs-lys_M_signal38.174526
Spike_AFFX-r2-P1-cre_3_signal4942.716797
Spike_AFFX-r2-Bs-lys_3-5-ratio1.305900
Spike_AFFX-r2-Bs-dap_M_signal339.031860
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.005466
Spike_AFFX-r2-Ec-bioB_avg-signal115.863075
Spike_AFFX-r2-Bs-thr_avg-signal235.211349
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1124.727295
Spike_AFFX-r2-Bs-phe_5_signal121.463150
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1407.749634
RawQ2.057789
Spike_AFFX-r2-Bs-lys_5_signal49.619156
Signal(A)4.308398
%A36.413853
Signal(All)146.002136
Corner+Avg:127,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal349.818817
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal124.394691
Spike_AFFX-r2-Ec-bioD_avg-signal1266.238525
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.911442
Spike_AFFX-r2-Bs-lys_avg-signal50.863773
Spike_AFFX-r2-P1-cre_avg-signal4439.157715
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.674704
Spike_AFFX-r2-Bs-thr_3_signal313.579041
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-signal107.463783
Spike_AFFX-r2-Bs-dap_3_signal429.109161
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.251636
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal361.986694
#M382
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal64.797638
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.966386
Spike_AFFX-r2-Bs-thr_M_signal235.692871
Signal(P)232.846573
Spike_AFFX-r2-Bs-phe_3-5-ratio1.024135
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10217,Count:9
Spike_AFFX-r2-P1-cre_5_signal3935.598633
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8306
Signal(M)16.398090
BackgroundAvg:48.83,Std:1.82,Min:45.2,Max:53.0
Spike_AFFX-r2-Ec-bioC_avg-signal355.902771
Spike_AFFX-r2-Bs-dap_avg-signal323.056793
Spike_AFFX-r2-Bs-dap_3-5-ratio2.134559
Spike_AFFX-r2-Ec-bioB_5_signal133.069992
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.200134
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-10_1mM-SA-treated_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 ("Pieterse_6241-10_1mM-SA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-10_1mM-SA-treated_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 1mM SA
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:1.537713
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-ratio1.150218
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.764454
Spike_AFFX-r2-Bs-dap_5_signal160.838623
NoiseAvg:1.74,Std:0.05,Min:1.6,Max:1.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal160.423874
#P13912
Spike_AFFX-r2-Bs-phe_M_signal72.380531
Corner-Avg:11263,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal138.495804
Spike_AFFX-r2-Ec-bioB_3_signal111.794029
Spike_AFFX-r2-Bs-lys_M_signal36.137836
Spike_AFFX-r2-P1-cre_3_signal5506.370605
Spike_AFFX-r2-Bs-lys_3-5-ratio2.730147
Spike_AFFX-r2-Bs-dap_M_signal306.512634
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.877205
Spike_AFFX-r2-Ec-bioB_avg-signal132.176712
Spike_AFFX-r2-Bs-thr_avg-signal232.541489
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1319.875000
Spike_AFFX-r2-Bs-phe_5_signal81.817284
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1707.264648
RawQ1.825431
Spike_AFFX-r2-Bs-lys_5_signal35.711102
Signal(A)4.929860
%A37.365192
Signal(All)147.767883
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal448.051971
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal99.947639
Spike_AFFX-r2-Ec-bioD_avg-signal1513.569824
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.990795
Spike_AFFX-r2-Bs-lys_avg-signal56.448498
Spike_AFFX-r2-P1-cre_avg-signal5146.805664
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_signal301.148438
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-signal84.715149
Spike_AFFX-r2-Bs-dap_3_signal408.556335
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.293505
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal432.841675
#M375
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal97.496544
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.035141
Spike_AFFX-r2-Bs-thr_M_signal236.052124
Signal(P)238.775482
Spike_AFFX-r2-Bs-phe_3-5-ratio1.221596
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9884,Count:9
Spike_AFFX-r2-P1-cre_5_signal4787.241211
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8523
Signal(M)17.929979
BackgroundAvg:43.58,Std:0.20,Min:43.0,Max:44.1
Spike_AFFX-r2-Ec-bioC_avg-signal440.446838
Spike_AFFX-r2-Bs-dap_avg-signal291.969208
Spike_AFFX-r2-Bs-dap_3-5-ratio2.540163
Spike_AFFX-r2-Ec-bioB_5_signal146.240311
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.537713
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-11_0.1mM-MeJA-treated_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 ("Pieterse_6241-11_0.1mM-MeJA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-11_0.1mM-MeJA-treated_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 0.1mM MeJA
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:1.125517
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-ratio1.376745
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.867819
Spike_AFFX-r2-Bs-dap_5_signal265.591492
NoiseAvg:2.10,Std:0.20,Min:1.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal141.726181
#P14322
Spike_AFFX-r2-Bs-phe_M_signal87.850761
Corner-Avg:12217,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.301300
Spike_AFFX-r2-Ec-bioB_3_signal97.971329
Spike_AFFX-r2-Bs-lys_M_signal46.471329
Spike_AFFX-r2-P1-cre_3_signal5438.205078
Spike_AFFX-r2-Bs-lys_3-5-ratio1.629237
Spike_AFFX-r2-Bs-dap_M_signal392.094666
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.908535
Spike_AFFX-r2-Ec-bioB_avg-signal110.055443
Spike_AFFX-r2-Bs-thr_avg-signal277.128571
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1072.096191
Spike_AFFX-r2-Bs-phe_5_signal103.851685
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1432.329224
RawQ2.090959
Spike_AFFX-r2-Bs-lys_5_signal50.697361
Signal(A)4.039059
%A35.686104
Signal(All)146.180344
Corner+Avg:109,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal413.095825
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal159.085831
Spike_AFFX-r2-Ec-bioD_avg-signal1252.212646
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.788250
Spike_AFFX-r2-Bs-lys_avg-signal59.922230
Spike_AFFX-r2-P1-cre_avg-signal4694.124512
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.525647
Spike_AFFX-r2-Bs-thr_3_signal412.215576
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-signal116.929420
Spike_AFFX-r2-Bs-dap_3_signal525.759338
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.336008
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal417.950134
#M348
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.598007
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.988385
Spike_AFFX-r2-Bs-thr_M_signal277.443939
Signal(P)230.138931
Spike_AFFX-r2-Bs-phe_3-5-ratio1.531856
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10594,Count:9
Spike_AFFX-r2-P1-cre_5_signal3950.044189
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8140
Signal(M)15.649415
BackgroundAvg:52.76,Std:0.37,Min:51.7,Max:53.5
Spike_AFFX-r2-Ec-bioC_avg-signal415.522980
Spike_AFFX-r2-Bs-dap_avg-signal394.481842
Spike_AFFX-r2-Bs-dap_3-5-ratio1.979579
Spike_AFFX-r2-Ec-bioB_5_signal112.893707
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.125517
NF1.000000
HZ4
Tau0.015000

Slide: Pieterse_6241-12_Bio1mM-SA-and-0.1-mM-MeJA-treated_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 ("Pieterse_6241-12_Bio1mM-SA-and-0.1-mM-MeJA-treated_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:

BioSource 1 Information

BioSource Name: Pieterse_6241-12_Bio1mM-SA-and-0.1-mM-MeJA-treated_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35
Growth Conditions:
stratificationSeeds were placed in water at 4 degrees Celsius for 48h prior to sowing
Growth protocolSeeds were sown in quartz sand. After two weeks, seedlings were transferred to 60-ml pots containing a sand/potting soil mixture that was autoclaved twice for 20 min and further cultivated in a growth chamber with an 8-h day (24C) and 16-h night (20C) at 70% R.H. for another 3 weeks.
LocationGrowth chamber
growthsubstrate typeNatural soil
Soil11 parts potting soil : 5 parts Quartz sand
Tissue: Whole rosette
in vivo Treatment:
TreatmentPlants are dipped in water containing 0.015% Silwet + 1mM SA + 0.1mM MeJA
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:1.349252
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-ratio1.409852
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.088472
Spike_AFFX-r2-Bs-dap_5_signal297.167603
NoiseAvg:2.13,Std:0.15,Min:1.9,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal144.508255
#P13709
Spike_AFFX-r2-Bs-phe_M_signal101.537384
Corner-Avg:10706,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal125.659973
Spike_AFFX-r2-Ec-bioB_3_signal122.547478
Spike_AFFX-r2-Bs-lys_M_signal47.760979
Spike_AFFX-r2-P1-cre_3_signal5642.769043
Spike_AFFX-r2-Bs-lys_3-5-ratio1.282814
Spike_AFFX-r2-Bs-dap_M_signal481.006622
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.694125
Spike_AFFX-r2-Ec-bioB_avg-signal120.264732
Spike_AFFX-r2-Bs-thr_avg-signal274.348083
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1068.840088
Spike_AFFX-r2-Bs-phe_5_signal116.594872
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1273.382446
RawQ2.046443
Spike_AFFX-r2-Bs-lys_5_signal64.615379
Signal(A)5.382693
%A38.154320
Signal(All)147.417358
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal398.576996
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal170.222397
Spike_AFFX-r2-Ec-bioD_avg-signal1171.111328
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.100834
Spike_AFFX-r2-Bs-lys_avg-signal65.088615
Spike_AFFX-r2-P1-cre_avg-signal4822.577148
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.744849
Spike_AFFX-r2-Bs-thr_3_signal389.323303
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-signal129.451553
Spike_AFFX-r2-Bs-dap_3_signal582.845459
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.191369
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal379.486359
#M398
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.889488
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.050307
Spike_AFFX-r2-Bs-thr_M_signal289.212708
Signal(P)241.274521
Spike_AFFX-r2-Bs-phe_3-5-ratio1.459948
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10156,Count:9
Spike_AFFX-r2-P1-cre_5_signal4002.384766
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8703
Signal(M)20.381575
BackgroundAvg:48.11,Std:1.92,Min:45.5,Max:56.4
Spike_AFFX-r2-Ec-bioC_avg-signal389.031677
Spike_AFFX-r2-Bs-dap_avg-signal453.673218
Spike_AFFX-r2-Bs-dap_3-5-ratio1.961336
Spike_AFFX-r2-Ec-bioB_5_signal112.586739
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.349252
NF1.000000
HZ4
Tau0.015000


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