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Experiment: Role of TGA factors in the salicylic acid/etylene crosstalk

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-569

The aim of this study is to check which ethylene-induced genes are suppressed by salicylic acid. In addition we want to elucidate the role of TGA factors in the ethylene signaling network and how they connect this pathway with the salicylic acid pathway. To adress this question we treated Col-0 plants and tga256 mutant plants with water, ACC, SA and SA/ACC for 12h.Zander et al., 2010, Plant J.

About the Experimenter

Name: Christiane Gatz
Head of Lab Name: Christiane Gatz
Lab:
Institute: Department of General and Molecular Physiology of the Plant Albrecht-von-Haller-Institute for Plant Sciences , Georg-August University Goettingen (University of Goettingen)
Address:
Untere Karsple 2, Goettingen, Niedersachsen
Postcode: 37073
Country: GERMANY
 
Telephone Number: 0049-551-3978
Fax Number: +49-551-39-7820

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, genetic_modification_design
Number of Slides:24
 
Experimental Parameters:
parameterhormone treatment
parametercompound_based_treatment
parametergenetic_modification_design
Quality Control Measures Taken:
References: Zander et al., 2010, Plant J.
 
Other Information:

Slides in this Experiment

Hybridisation Set: Gatz: Role of TGA factors in the salicylic acid/etylene crosstalk

Slide: Gatz_569-1_Col-0_mock_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 ("Gatz_569-1_Col-0_mock_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: Gatz_569-1_Col-0_mock_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with water and harvested after 12h
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.474004
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-ratio1.376458
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.526749
Spike_AFFX-r2-Bs-dap_5_signal61.088799
NoiseAvg:4.36,Std:0.23,Min:3.9,Max:5.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.133266
#P13660
Spike_AFFX-r2-Bs-phe_M_signal22.378090
Corner-Avg:26283,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.190208
Spike_AFFX-r2-Ec-bioB_3_signal84.110725
Spike_AFFX-r2-Bs-lys_M_signal13.269923
Spike_AFFX-r2-P1-cre_3_signal4529.021484
Spike_AFFX-r2-Bs-lys_3-5-ratio1.609820
Spike_AFFX-r2-Bs-dap_M_signal167.006210
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.816811
Spike_AFFX-r2-Ec-bioB_avg-signal79.464104
Spike_AFFX-r2-Bs-thr_avg-signal46.172222
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal906.808472
Spike_AFFX-r2-Bs-phe_5_signal17.251371
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1279.231445
RawQ3.565959
Spike_AFFX-r2-Bs-lys_5_signal21.707470
Signal(A)5.174225
%A38.132397
Signal(All)147.640488
Corner+Avg:422,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal271.092255
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.312222
Spike_AFFX-r2-Ec-bioD_avg-signal1093.020020
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.886013
Spike_AFFX-r2-Bs-lys_avg-signal23.307503
Spike_AFFX-r2-P1-cre_avg-signal3909.683594
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.981587
Spike_AFFX-r2-Bs-thr_3_signal54.746464
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.980560
Spike_AFFX-r2-Bs-dap_3_signal213.556976
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.410696
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal231.662720
#M452
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.945114
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.170202
Spike_AFFX-r2-Bs-thr_M_signal53.636932
Signal(P)242.633713
Spike_AFFX-r2-Bs-phe_3-5-ratio1.873023
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:20716,Count:9
Spike_AFFX-r2-P1-cre_5_signal3290.345459
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8698
Signal(M)18.357584
BackgroundAvg:90.77,Std:0.85,Min:89.0,Max:92.8
Spike_AFFX-r2-Ec-bioC_avg-signal251.377487
Spike_AFFX-r2-Bs-dap_avg-signal147.217331
Spike_AFFX-r2-Bs-dap_3-5-ratio3.495845
Spike_AFFX-r2-Ec-bioB_5_signal55.091385
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.474004
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-2_Col-0_mock_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 ("Gatz_569-2_Col-0_mock_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-2_Col-0_mock_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with water and harvested after 12h
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.699554
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-ratio1.310239
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.164801
Spike_AFFX-r2-Bs-dap_5_signal114.405205
NoiseAvg:2.87,Std:0.09,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal39.525475
#P13611
Spike_AFFX-r2-Bs-phe_M_signal44.952404
Corner-Avg:18465,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal136.091003
Spike_AFFX-r2-Ec-bioB_3_signal98.700287
Spike_AFFX-r2-Bs-lys_M_signal24.489321
Spike_AFFX-r2-P1-cre_3_signal7126.421387
Spike_AFFX-r2-Bs-lys_3-5-ratio1.966444
Spike_AFFX-r2-Bs-dap_M_signal292.897766
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.482219
Spike_AFFX-r2-Ec-bioB_avg-signal106.509026
Spike_AFFX-r2-Bs-thr_avg-signal88.787254
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1461.677246
Spike_AFFX-r2-Bs-phe_5_signal65.201920
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2023.133179
RawQ2.656799
Spike_AFFX-r2-Bs-lys_5_signal33.009758
Signal(A)4.885034
%A38.382290
Signal(All)152.411011
Corner+Avg:302,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal364.807983
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.782391
Spike_AFFX-r2-Ec-bioD_avg-signal1742.405273
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.671196
Spike_AFFX-r2-Bs-lys_avg-signal40.803642
Spike_AFFX-r2-P1-cre_avg-signal6282.723633
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.946515
Spike_AFFX-r2-Bs-thr_3_signal137.636337
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-signal57.312237
Spike_AFFX-r2-Bs-dap_3_signal489.267670
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.384118
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal313.592865
#M444
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal64.911850
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.163317
Spike_AFFX-r2-Bs-thr_M_signal89.199944
Signal(P)251.659546
Spike_AFFX-r2-Bs-phe_3-5-ratio0.947555
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14264,Count:9
Spike_AFFX-r2-P1-cre_5_signal5439.025391
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8755
Signal(M)18.893408
BackgroundAvg:61.53,Std:0.53,Min:59.6,Max:62.8
Spike_AFFX-r2-Ec-bioC_avg-signal339.200439
Spike_AFFX-r2-Bs-dap_avg-signal298.856873
Spike_AFFX-r2-Bs-dap_3-5-ratio4.276621
Spike_AFFX-r2-Ec-bioB_5_signal84.735786
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.699554
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-3_Col-0_mock_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 ("Gatz_569-3_Col-0_mock_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-3_Col-0_mock_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with water and harvested after 12h
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.655288
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-ratio1.225151
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.570973
Spike_AFFX-r2-Bs-dap_5_signal101.094910
NoiseAvg:2.78,Std:0.05,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal41.008461
#P13943
Spike_AFFX-r2-Bs-phe_M_signal39.186817
Corner-Avg:18430,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal141.629364
Spike_AFFX-r2-Ec-bioB_3_signal131.259048
Spike_AFFX-r2-Bs-lys_M_signal26.796124
Spike_AFFX-r2-P1-cre_3_signal6476.434570
Spike_AFFX-r2-Bs-lys_3-5-ratio1.982515
Spike_AFFX-r2-Bs-dap_M_signal246.734314
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.833332
Spike_AFFX-r2-Ec-bioB_avg-signal118.813721
Spike_AFFX-r2-Bs-thr_avg-signal81.150536
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1334.488892
Spike_AFFX-r2-Bs-phe_5_signal44.757587
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2007.605591
RawQ2.643229
Spike_AFFX-r2-Bs-lys_5_signal23.499628
Signal(A)4.535157
%A37.023235
Signal(All)151.825790
Corner+Avg:282,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal387.254852
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal73.027924
Spike_AFFX-r2-Ec-bioD_avg-signal1671.047241
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.126698
Spike_AFFX-r2-Bs-lys_avg-signal32.294701
Spike_AFFX-r2-P1-cre_avg-signal5881.334961
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.850066
Spike_AFFX-r2-Bs-thr_3_signal116.190582
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-signal52.324108
Spike_AFFX-r2-Bs-dap_3_signal375.421234
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.504400
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal321.269379
#M422
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.588352
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.205390
Spike_AFFX-r2-Bs-thr_M_signal86.252556
Signal(P)245.124161
Spike_AFFX-r2-Bs-phe_3-5-ratio1.631632
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16270,Count:9
Spike_AFFX-r2-P1-cre_5_signal5286.235352
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8445
Signal(M)16.778526
BackgroundAvg:60.93,Std:0.29,Min:59.9,Max:61.8
Spike_AFFX-r2-Ec-bioC_avg-signal354.262115
Spike_AFFX-r2-Bs-dap_avg-signal241.083481
Spike_AFFX-r2-Bs-dap_3-5-ratio3.713552
Spike_AFFX-r2-Ec-bioB_5_signal83.552727
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.655288
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-4_Col-0_SA_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 ("Gatz_569-4_Col-0_SA_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: Gatz_569-4_Col-0_SA_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM SA
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.479053
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-ratio1.464030
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.811940
Spike_AFFX-r2-Bs-dap_5_signal127.012428
NoiseAvg:3.86,Std:0.14,Min:3.6,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal50.902828
#P13775
Spike_AFFX-r2-Bs-phe_M_signal47.196949
Corner-Avg:24912,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal95.358788
Spike_AFFX-r2-Ec-bioB_3_signal54.527111
Spike_AFFX-r2-Bs-lys_M_signal26.851940
Spike_AFFX-r2-P1-cre_3_signal4371.232422
Spike_AFFX-r2-Bs-lys_3-5-ratio1.732511
Spike_AFFX-r2-Bs-dap_M_signal253.508514
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.643946
Spike_AFFX-r2-Ec-bioB_avg-signal72.347504
Spike_AFFX-r2-Bs-thr_avg-signal94.617096
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal826.257080
Spike_AFFX-r2-Bs-phe_5_signal44.100883
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1245.547363
RawQ3.129225
Spike_AFFX-r2-Bs-lys_5_signal30.852139
Signal(A)4.705048
%A37.720299
Signal(All)144.685013
Corner+Avg:398,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal251.324860
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal77.765442
Spike_AFFX-r2-Ec-bioD_avg-signal1035.902222
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.390179
Spike_AFFX-r2-Bs-lys_avg-signal37.051922
Spike_AFFX-r2-P1-cre_avg-signal3678.493164
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.889522
Spike_AFFX-r2-Bs-thr_3_signal134.584335
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-signal56.354420
Spike_AFFX-r2-Bs-dap_3_signal428.329315
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.507457
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal212.612473
#M431
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.451675
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.182080
Spike_AFFX-r2-Bs-thr_M_signal98.364128
Signal(P)236.071732
Spike_AFFX-r2-Bs-phe_3-5-ratio1.763353
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:19848,Count:9
Spike_AFFX-r2-P1-cre_5_signal2985.753906
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8604
Signal(M)18.318026
BackgroundAvg:78.27,Std:0.80,Min:76.4,Max:79.7
Spike_AFFX-r2-Ec-bioC_avg-signal231.968658
Spike_AFFX-r2-Bs-dap_avg-signal269.616760
Spike_AFFX-r2-Bs-dap_3-5-ratio3.372342
Spike_AFFX-r2-Ec-bioB_5_signal67.156616
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.479053
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-5_Col-0_SA_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 ("Gatz_569-5_Col-0_SA_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-5_Col-0_SA_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM SA
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.700753
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-ratio1.385000
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.389964
Spike_AFFX-r2-Bs-dap_5_signal125.274521
NoiseAvg:2.53,Std:0.05,Min:2.4,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_signal38.343052
#P13687
Spike_AFFX-r2-Bs-phe_M_signal51.944298
Corner-Avg:16052,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal129.335754
Spike_AFFX-r2-Ec-bioB_3_signal90.943871
Spike_AFFX-r2-Bs-lys_M_signal29.912678
Spike_AFFX-r2-P1-cre_3_signal6442.975586
Spike_AFFX-r2-Bs-lys_3-5-ratio2.510664
Spike_AFFX-r2-Bs-dap_M_signal275.324005
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.654058
Spike_AFFX-r2-Ec-bioB_avg-signal95.236183
Spike_AFFX-r2-Bs-thr_avg-signal122.829216
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1237.437866
Spike_AFFX-r2-Bs-phe_5_signal71.545158
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1761.395996
RawQ2.431541
Spike_AFFX-r2-Bs-lys_5_signal31.391682
Signal(A)4.593704
%A38.128014
Signal(All)147.311462
Corner+Avg:257,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal351.083374
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal99.535133
Spike_AFFX-r2-Ec-bioD_avg-signal1499.416992
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.004383
Spike_AFFX-r2-Bs-lys_avg-signal46.706112
Spike_AFFX-r2-P1-cre_avg-signal5547.471680
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.867602
Spike_AFFX-r2-Bs-thr_3_signal216.793823
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-signal74.341530
Spike_AFFX-r2-Bs-dap_3_signal617.450317
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.423422
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal297.615051
#M426
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal78.813980
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.179656
Spike_AFFX-r2-Bs-thr_M_signal113.350754
Signal(P)242.055954
Spike_AFFX-r2-Bs-phe_3-5-ratio1.391221
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12346,Count:9
Spike_AFFX-r2-P1-cre_5_signal4651.968262
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8697
Signal(M)16.908813
BackgroundAvg:55.25,Std:0.29,Min:54.6,Max:56.3
Spike_AFFX-r2-Ec-bioC_avg-signal324.349213
Spike_AFFX-r2-Bs-dap_avg-signal339.349609
Spike_AFFX-r2-Bs-dap_3-5-ratio4.928778
Spike_AFFX-r2-Ec-bioB_5_signal65.428940
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.700753
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-6_Col-0_SA_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 ("Gatz_569-6_Col-0_SA_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-6_Col-0_SA_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM SA
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.703395
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-ratio1.279596
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.860489
Spike_AFFX-r2-Bs-dap_5_signal121.713524
NoiseAvg:2.47,Std:0.08,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal49.039272
#P13890
Spike_AFFX-r2-Bs-phe_M_signal49.656578
Corner-Avg:19936,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal166.949539
Spike_AFFX-r2-Ec-bioB_3_signal97.427032
Spike_AFFX-r2-Bs-lys_M_signal27.474342
Spike_AFFX-r2-P1-cre_3_signal6997.518555
Spike_AFFX-r2-Bs-lys_3-5-ratio1.843516
Spike_AFFX-r2-Bs-dap_M_signal317.766632
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.685903
Spike_AFFX-r2-Ec-bioB_avg-signal125.866463
Spike_AFFX-r2-Bs-thr_avg-signal111.220680
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1487.873047
Spike_AFFX-r2-Bs-phe_5_signal75.187820
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2005.796143
RawQ2.242855
Spike_AFFX-r2-Bs-lys_5_signal32.917576
Signal(A)4.617609
%A37.176678
Signal(All)150.881744
Corner+Avg:312,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal389.699493
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal85.290169
Spike_AFFX-r2-Ec-bioD_avg-signal1746.834595
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.894344
Spike_AFFX-r2-Bs-lys_avg-signal40.358669
Spike_AFFX-r2-P1-cre_avg-signal6233.028320
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.928979
Spike_AFFX-r2-Bs-thr_3_signal180.753998
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-signal70.044853
Spike_AFFX-r2-Bs-dap_3_signal513.270386
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.348096
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal355.737061
#M440
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.684086
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.095471
Spike_AFFX-r2-Bs-thr_M_signal103.868782
Signal(P)244.422852
Spike_AFFX-r2-Bs-phe_3-5-ratio1.134362
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15356,Count:9
Spike_AFFX-r2-P1-cre_5_signal5468.538574
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8480
Signal(M)16.867868
BackgroundAvg:52.21,Std:0.23,Min:51.6,Max:53.0
Spike_AFFX-r2-Ec-bioC_avg-signal372.718262
Spike_AFFX-r2-Bs-dap_avg-signal317.583496
Spike_AFFX-r2-Bs-dap_3-5-ratio4.217037
Spike_AFFX-r2-Ec-bioB_5_signal113.222816
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.703395
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-7_Col-0_ACC_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 ("Gatz_569-7_Col-0_ACC_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: Gatz_569-7_Col-0_ACC_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with 1mM ACC and harvested after 12h
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.418336
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-ratio1.369979
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.960866
Spike_AFFX-r2-Bs-dap_5_signal95.169228
NoiseAvg:3.99,Std:0.18,Min:3.6,Max:4.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal36.798248
#P14046
Spike_AFFX-r2-Bs-phe_M_signal40.831333
Corner-Avg:26219,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.058289
Spike_AFFX-r2-Ec-bioB_3_signal67.099648
Spike_AFFX-r2-Bs-lys_M_signal25.278633
Spike_AFFX-r2-P1-cre_3_signal4377.506836
Spike_AFFX-r2-Bs-lys_3-5-ratio1.295639
Spike_AFFX-r2-Bs-dap_M_signal247.088943
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.336464
Spike_AFFX-r2-Ec-bioB_avg-signal76.663460
Spike_AFFX-r2-Bs-thr_avg-signal66.936760
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal849.474365
Spike_AFFX-r2-Bs-phe_5_signal49.683567
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1240.841675
RawQ3.198779
Spike_AFFX-r2-Bs-lys_5_signal25.378019
Signal(A)4.225819
%A36.725121
Signal(All)144.152802
Corner+Avg:556,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal266.443298
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal65.936081
Spike_AFFX-r2-Ec-bioD_avg-signal1045.157959
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.578255
Spike_AFFX-r2-Bs-lys_avg-signal27.845797
Spike_AFFX-r2-P1-cre_avg-signal3786.407715
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.696624
Spike_AFFX-r2-Bs-thr_3_signal85.977791
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-signal52.150326
Spike_AFFX-r2-Bs-dap_3_signal363.746368
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.460717
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.749969
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.880741
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.111338
Spike_AFFX-r2-Bs-thr_M_signal78.034241
Signal(P)231.130600
Spike_AFFX-r2-Bs-phe_3-5-ratio1.327121
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:21351,Count:9
Spike_AFFX-r2-P1-cre_5_signal3195.308838
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8377
Signal(M)16.188751
BackgroundAvg:80.79,Std:1.12,Min:78.1,Max:83.7
Spike_AFFX-r2-Ec-bioC_avg-signal253.096634
Spike_AFFX-r2-Bs-dap_avg-signal235.334854
Spike_AFFX-r2-Bs-dap_3-5-ratio3.822101
Spike_AFFX-r2-Ec-bioB_5_signal69.832451
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.418336
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-8_Col-0_ACC_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 ("Gatz_569-8_Col-0_ACC_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-8_Col-0_ACC_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with 1mM ACC and harvested after 12h
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.588075
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-ratio1.223325
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.165223
Spike_AFFX-r2-Bs-dap_5_signal102.547058
NoiseAvg:2.79,Std:0.10,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal33.334225
#P13849
Spike_AFFX-r2-Bs-phe_M_signal38.235069
Corner-Avg:18707,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.399178
Spike_AFFX-r2-Ec-bioB_3_signal101.531555
Spike_AFFX-r2-Bs-lys_M_signal19.989273
Spike_AFFX-r2-P1-cre_3_signal5674.856934
Spike_AFFX-r2-Bs-lys_3-5-ratio1.705528
Spike_AFFX-r2-Bs-dap_M_signal221.331329
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.708786
Spike_AFFX-r2-Ec-bioB_avg-signal104.355194
Spike_AFFX-r2-Bs-thr_avg-signal68.797646
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1167.512573
Spike_AFFX-r2-Bs-phe_5_signal31.039282
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1958.448364
RawQ2.480823
Spike_AFFX-r2-Bs-lys_5_signal26.686560
Signal(A)4.194988
%A37.553703
Signal(All)149.496841
Corner+Avg:311,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal359.744690
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal74.953224
Spike_AFFX-r2-Ec-bioD_avg-signal1562.980469
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.714600
Spike_AFFX-r2-Bs-lys_avg-signal30.730169
Spike_AFFX-r2-P1-cre_avg-signal5156.868164
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.731697
Spike_AFFX-r2-Bs-thr_3_signal90.295280
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-signal48.075855
Spike_AFFX-r2-Bs-dap_3_signal363.741852
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.677454
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal260.207642
#M395
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.514671
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.382529
Spike_AFFX-r2-Bs-thr_M_signal82.763435
Signal(P)243.161865
Spike_AFFX-r2-Bs-phe_3-5-ratio2.414786
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15615,Count:9
Spike_AFFX-r2-P1-cre_5_signal4638.879395
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8566
Signal(M)16.556948
BackgroundAvg:57.50,Std:0.37,Min:56.4,Max:58.7
Spike_AFFX-r2-Ec-bioC_avg-signal309.976166
Spike_AFFX-r2-Bs-dap_avg-signal229.206741
Spike_AFFX-r2-Bs-dap_3-5-ratio3.547072
Spike_AFFX-r2-Ec-bioB_5_signal87.134857
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.588075
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-9_Col-0_ACC_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 ("Gatz_569-9_Col-0_ACC_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-9_Col-0_ACC_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with 1mM ACC and harvested after 12h
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.632914
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-ratio1.232277
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.138673
Spike_AFFX-r2-Bs-dap_5_signal74.777802
NoiseAvg:2.85,Std:0.07,Min:2.7,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal27.468121
#P14030
Spike_AFFX-r2-Bs-phe_M_signal29.023293
Corner-Avg:19430,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.343590
Spike_AFFX-r2-Ec-bioB_3_signal99.898590
Spike_AFFX-r2-Bs-lys_M_signal18.488924
Spike_AFFX-r2-P1-cre_3_signal5034.269531
Spike_AFFX-r2-Bs-lys_3-5-ratio1.110692
Spike_AFFX-r2-Bs-dap_M_signal173.869324
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.442872
Spike_AFFX-r2-Ec-bioB_avg-signal103.991547
Spike_AFFX-r2-Bs-thr_avg-signal51.799667
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal936.444824
Spike_AFFX-r2-Bs-phe_5_signal35.210892
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1609.702881
RawQ2.523175
Spike_AFFX-r2-Bs-lys_5_signal22.304127
Signal(A)4.817201
%A36.606750
Signal(All)144.458710
Corner+Avg:294,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal300.674744
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.660778
Spike_AFFX-r2-Ec-bioD_avg-signal1273.073853
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.508110
Spike_AFFX-r2-Bs-lys_avg-signal21.855356
Spike_AFFX-r2-P1-cre_avg-signal4559.804199
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal67.101112
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal36.298321
Spike_AFFX-r2-Bs-dap_3_signal284.526917
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.718951
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal316.273773
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.773024
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.950679
Spike_AFFX-r2-Bs-thr_M_signal60.829773
Signal(P)231.509781
Spike_AFFX-r2-Bs-phe_3-5-ratio1.268380
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16334,Count:9
Spike_AFFX-r2-P1-cre_5_signal4085.338867
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8350
Signal(M)15.807880
BackgroundAvg:57.41,Std:0.37,Min:56.6,Max:58.6
Spike_AFFX-r2-Ec-bioC_avg-signal308.474243
Spike_AFFX-r2-Bs-dap_avg-signal177.724686
Spike_AFFX-r2-Bs-dap_3-5-ratio3.804965
Spike_AFFX-r2-Ec-bioB_5_signal87.732460
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.632914
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-10_Col-0_SA+ACC_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 ("Gatz_569-10_Col-0_SA+ACC_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: Gatz_569-10_Col-0_SA+ACC_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC and 1mM SA
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.455099
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-ratio1.252894
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.236623
Spike_AFFX-r2-Bs-dap_5_signal128.802185
NoiseAvg:3.55,Std:0.12,Min:3.2,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal42.761997
#P14093
Spike_AFFX-r2-Bs-phe_M_signal46.806919
Corner-Avg:25963,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal108.589706
Spike_AFFX-r2-Ec-bioB_3_signal99.105476
Spike_AFFX-r2-Bs-lys_M_signal24.798899
Spike_AFFX-r2-P1-cre_3_signal4334.517090
Spike_AFFX-r2-Bs-lys_3-5-ratio1.701130
Spike_AFFX-r2-Bs-dap_M_signal265.394104
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.646725
Spike_AFFX-r2-Ec-bioB_avg-signal95.945740
Spike_AFFX-r2-Bs-thr_avg-signal84.414482
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal922.142944
Spike_AFFX-r2-Bs-phe_5_signal63.654640
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1299.330444
RawQ3.075108
Spike_AFFX-r2-Bs-lys_5_signal27.122135
Signal(A)3.961814
%A36.523453
Signal(All)141.019165
Corner+Avg:408,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal315.534698
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal71.836739
Spike_AFFX-r2-Ec-bioD_avg-signal1110.736694
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.784306
Spike_AFFX-r2-Bs-lys_avg-signal32.686436
Spike_AFFX-r2-P1-cre_avg-signal3897.061035
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.692240
Spike_AFFX-r2-Bs-thr_3_signal113.179237
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-signal60.766102
Spike_AFFX-r2-Bs-dap_3_signal441.510101
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.409034
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal229.740540
#M386
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.138279
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.373439
Spike_AFFX-r2-Bs-thr_M_signal97.302216
Signal(P)225.505829
Spike_AFFX-r2-Bs-phe_3-5-ratio1.128539
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:23161,Count:9
Spike_AFFX-r2-P1-cre_5_signal3459.604980
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8331
Signal(M)14.475897
BackgroundAvg:72.78,Std:0.94,Min:70.3,Max:74.7
Spike_AFFX-r2-Ec-bioC_avg-signal272.637634
Spike_AFFX-r2-Bs-dap_avg-signal278.568787
Spike_AFFX-r2-Bs-dap_3-5-ratio3.427815
Spike_AFFX-r2-Ec-bioB_5_signal80.142036
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.455099
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-11_Col-0_SA+ACC_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 ("Gatz_569-11_Col-0_SA+ACC_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-11_Col-0_SA+ACC_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC and 1mM SA
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.408011
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-ratio1.434666
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.963891
Spike_AFFX-r2-Bs-dap_5_signal62.794724
NoiseAvg:3.19,Std:0.10,Min:2.8,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.496300
#P14323
Spike_AFFX-r2-Bs-phe_M_signal23.707094
Corner-Avg:18959,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal103.792122
Spike_AFFX-r2-Ec-bioB_3_signal63.258198
Spike_AFFX-r2-Bs-lys_M_signal18.462978
Spike_AFFX-r2-P1-cre_3_signal4198.200684
Spike_AFFX-r2-Bs-lys_3-5-ratio1.844669
Spike_AFFX-r2-Bs-dap_M_signal194.049927
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.433741
Spike_AFFX-r2-Ec-bioB_avg-signal77.559418
Spike_AFFX-r2-Bs-thr_avg-signal63.811329
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal704.307007
Spike_AFFX-r2-Bs-phe_5_signal29.160759
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1222.332642
RawQ2.665872
Spike_AFFX-r2-Bs-lys_5_signal21.381809
Signal(A)3.419540
%A35.335381
Signal(All)137.869553
Corner+Avg:315,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal242.922012
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal58.769497
Spike_AFFX-r2-Ec-bioD_avg-signal963.319824
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.792633
Spike_AFFX-r2-Bs-lys_avg-signal26.429049
Spike_AFFX-r2-P1-cre_avg-signal3562.228516
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.871986
Spike_AFFX-r2-Bs-thr_3_signal97.848915
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal37.212452
Spike_AFFX-r2-Bs-dap_3_signal335.312561
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.735511
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal209.468842
#M427
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.442360
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.159705
Spike_AFFX-r2-Bs-thr_M_signal65.088776
Signal(P)217.218414
Spike_AFFX-r2-Bs-phe_3-5-ratio2.015363
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15738,Count:9
Spike_AFFX-r2-P1-cre_5_signal2926.256592
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8060
Signal(M)14.106777
BackgroundAvg:61.18,Std:0.48,Min:59.5,Max:62.2
Spike_AFFX-r2-Ec-bioC_avg-signal226.195435
Spike_AFFX-r2-Bs-dap_avg-signal197.385742
Spike_AFFX-r2-Bs-dap_3-5-ratio5.339821
Spike_AFFX-r2-Ec-bioB_5_signal65.627937
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.408011
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-12_Col-0_SA+ACC_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 ("Gatz_569-12_Col-0_SA+ACC_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Gatz_569-12_Col-0_SA+ACC_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC and 1mM SA
Additional Organism Information:
Sample Description8 treated single-grown plants are one sample
Other Information:
ecotype_habitat

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:0.705727
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-ratio1.405136
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.824567
Spike_AFFX-r2-Bs-dap_5_signal105.518959
NoiseAvg:2.82,Std:0.08,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal43.442249
#P13637
Spike_AFFX-r2-Bs-phe_M_signal48.021042
Corner-Avg:17593,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal160.970856
Spike_AFFX-r2-Ec-bioB_3_signal82.913704
Spike_AFFX-r2-Bs-lys_M_signal30.317337
Spike_AFFX-r2-P1-cre_3_signal6814.742188
Spike_AFFX-r2-Bs-lys_3-5-ratio1.825121
Spike_AFFX-r2-Bs-dap_M_signal235.542313
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.077849
Spike_AFFX-r2-Ec-bioB_avg-signal114.812950
Spike_AFFX-r2-Bs-thr_avg-signal88.058952
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1307.261230
Spike_AFFX-r2-Bs-phe_5_signal53.454563
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1840.215332
RawQ2.622971
Spike_AFFX-r2-Bs-lys_5_signal29.911386
Signal(A)5.264565
%A38.277073
Signal(All)146.733109
Corner+Avg:289,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal338.127411
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal43.226604
Spike_AFFX-r2-Ec-bioD_avg-signal1573.738281
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.785183
Spike_AFFX-r2-Bs-lys_avg-signal38.273537
Spike_AFFX-r2-P1-cre_avg-signal5832.310547
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.937747
Spike_AFFX-r2-Bs-thr_3_signal133.708679
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-signal48.234070
Spike_AFFX-r2-Bs-dap_3_signal456.141479
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.407688
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal311.740814
#M442
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal54.591892
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.084643
Spike_AFFX-r2-Bs-thr_M_signal87.025902
Signal(P)241.459808
Spike_AFFX-r2-Bs-phe_3-5-ratio0.808661
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13083,Count:9
Spike_AFFX-r2-P1-cre_5_signal4849.879395
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8731
Signal(M)18.619793
BackgroundAvg:61.72,Std:0.26,Min:60.7,Max:62.4
Spike_AFFX-r2-Ec-bioC_avg-signal324.934113
Spike_AFFX-r2-Bs-dap_avg-signal265.734253
Spike_AFFX-r2-Bs-dap_3-5-ratio4.322839
Spike_AFFX-r2-Ec-bioB_5_signal100.554291
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.705727
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-13_tga256_mock_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 ("Gatz_569-13_tga256_mock_Rep1_ATH1") was made from "" 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: Gatz_569-13_tga256_mock_Rep1_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with water and harvested after 12h
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:0.539848
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-ratio1.306111
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.201630
Spike_AFFX-r2-Bs-dap_5_signal86.801888
NoiseAvg:3.74,Std:0.13,Min:3.4,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.151333
#P13618
Spike_AFFX-r2-Bs-phe_M_signal43.796284
Corner-Avg:25179,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.390244
Spike_AFFX-r2-Ec-bioB_3_signal98.493362
Spike_AFFX-r2-Bs-lys_M_signal13.500385
Spike_AFFX-r2-P1-cre_3_signal4378.342773
Spike_AFFX-r2-Bs-lys_3-5-ratio1.097176
Spike_AFFX-r2-Bs-dap_M_signal220.768845
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.232072
Spike_AFFX-r2-Ec-bioB_avg-signal91.283363
Spike_AFFX-r2-Bs-thr_avg-signal51.802967
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal767.879150
Spike_AFFX-r2-Bs-phe_5_signal32.298012
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1167.929077
RawQ3.153232
Spike_AFFX-r2-Bs-lys_5_signal24.506710
Signal(A)5.394068
%A38.369137
Signal(All)147.880890
Corner+Avg:394,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal252.668610
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal42.861683
Spike_AFFX-r2-Ec-bioD_avg-signal967.904114
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.701885
Spike_AFFX-r2-Bs-lys_avg-signal21.631760
Spike_AFFX-r2-P1-cre_avg-signal3865.270020
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.928979
Spike_AFFX-r2-Bs-thr_3_signal67.299957
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal39.651993
Spike_AFFX-r2-Bs-dap_3_signal270.676331
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.520980
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal222.135513
#M440
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.888186
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.137453
Spike_AFFX-r2-Bs-thr_M_signal57.957607
Signal(P)243.583237
Spike_AFFX-r2-Bs-phe_3-5-ratio1.327069
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:21730,Count:9
Spike_AFFX-r2-P1-cre_5_signal3352.197510
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8752
Signal(M)20.085529
BackgroundAvg:79.16,Std:0.74,Min:77.4,Max:80.9
Spike_AFFX-r2-Ec-bioC_avg-signal237.402069
Spike_AFFX-r2-Bs-dap_avg-signal192.749023
Spike_AFFX-r2-Bs-dap_3-5-ratio3.118323
Spike_AFFX-r2-Ec-bioB_5_signal81.966492
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.539848
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-14_tga256_mock_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 ("Gatz_569-14_tga256_mock_Rep2_ATH1") was made from "" 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: Gatz_569-14_tga256_mock_Rep2_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with water and harvested after 12h
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:0.532059
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-ratio1.024186
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.260194
Spike_AFFX-r2-Bs-dap_5_signal34.085304
NoiseAvg:2.30,Std:0.09,Min:2.1,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.963884
#P15149
Spike_AFFX-r2-Bs-phe_M_signal17.024441
Corner-Avg:10867,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal111.184090
Spike_AFFX-r2-Ec-bioB_3_signal87.210938
Spike_AFFX-r2-Bs-lys_M_signal5.268374
Spike_AFFX-r2-P1-cre_3_signal3451.090332
Spike_AFFX-r2-Bs-lys_3-5-ratio2.600857
Spike_AFFX-r2-Bs-dap_M_signal74.252594
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.273098
Spike_AFFX-r2-Ec-bioB_avg-signal89.199799
Spike_AFFX-r2-Bs-thr_avg-signal31.218241
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal655.878113
Spike_AFFX-r2-Bs-phe_5_signal15.006368
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1101.718872
RawQ2.261621
Spike_AFFX-r2-Bs-lys_5_signal8.541417
Signal(A)3.167482
%A31.994740
Signal(All)140.116409
Corner+Avg:166,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal275.464508
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.587299
Spike_AFFX-r2-Ec-bioD_avg-signal878.798462
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.413857
Spike_AFFX-r2-Bs-lys_avg-signal12.008264
Spike_AFFX-r2-P1-cre_avg-signal3410.341309
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal38.560574
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.206036
Spike_AFFX-r2-Bs-dap_3_signal130.843582
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.679762
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal238.349182
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.215002
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.155718
Spike_AFFX-r2-Bs-thr_M_signal38.130264
Signal(P)209.154495
Spike_AFFX-r2-Bs-phe_3-5-ratio1.705096
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8961,Count:9
Spike_AFFX-r2-P1-cre_5_signal3369.592041
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7298
Signal(M)12.279975
BackgroundAvg:52.15,Std:0.43,Min:50.9,Max:53.4
Spike_AFFX-r2-Ec-bioC_avg-signal256.906860
Spike_AFFX-r2-Bs-dap_avg-signal79.727165
Spike_AFFX-r2-Bs-dap_3-5-ratio3.838710
Spike_AFFX-r2-Ec-bioB_5_signal69.204369
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.532059
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-15_tga256_mock_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 ("Gatz_569-15_tga256_mock_Rep3_ATH1") was made from "" 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: Gatz_569-15_tga256_mock_Rep3_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants were sprayed with water and harvested after 12h
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:0.684427
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-ratio1.380171
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.850376
Spike_AFFX-r2-Bs-dap_5_signal125.365707
NoiseAvg:2.87,Std:0.09,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal50.487225
#P13153
Spike_AFFX-r2-Bs-phe_M_signal50.885204
Corner-Avg:21189,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal156.599991
Spike_AFFX-r2-Ec-bioB_3_signal101.560249
Spike_AFFX-r2-Bs-lys_M_signal27.250078
Spike_AFFX-r2-P1-cre_3_signal7459.863281
Spike_AFFX-r2-Bs-lys_3-5-ratio1.990930
Spike_AFFX-r2-Bs-dap_M_signal298.812836
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.020886
Spike_AFFX-r2-Ec-bioB_avg-signal125.863342
Spike_AFFX-r2-Bs-thr_avg-signal100.272552
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1538.926880
Spike_AFFX-r2-Bs-phe_5_signal53.053902
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2124.136230
RawQ2.553004
Spike_AFFX-r2-Bs-lys_5_signal35.891201
Signal(A)5.661061
%A40.026306
Signal(All)157.962265
Corner+Avg:338,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal404.670532
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal76.496933
Spike_AFFX-r2-Ec-bioD_avg-signal1831.531494
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.663307
Spike_AFFX-r2-Bs-lys_avg-signal44.866043
Spike_AFFX-r2-P1-cre_avg-signal6432.446289
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.310390
Spike_AFFX-r2-Bs-thr_3_signal152.516144
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-signal60.145344
Spike_AFFX-r2-Bs-dap_3_signal527.986023
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.380271
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal344.360748
#M527
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal71.456856
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.175135
Spike_AFFX-r2-Bs-thr_M_signal97.814293
Signal(P)269.161255
Spike_AFFX-r2-Bs-phe_3-5-ratio1.441872
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:17477,Count:9
Spike_AFFX-r2-P1-cre_5_signal5405.029785
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9130
Signal(M)21.168566
BackgroundAvg:59.70,Std:0.66,Min:58.2,Max:61.1
Spike_AFFX-r2-Ec-bioC_avg-signal374.515625
Spike_AFFX-r2-Bs-dap_avg-signal317.388184
Spike_AFFX-r2-Bs-dap_3-5-ratio4.211566
Spike_AFFX-r2-Ec-bioB_5_signal119.429779
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.684427
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-16_tga256_SA_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 ("Gatz_569-16_tga256_SA_Rep1_ATH1") was made from "" 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: Gatz_569-16_tga256_SA_Rep1_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 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:0.282007
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-ratio1.337628
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.096058
Spike_AFFX-r2-Bs-dap_5_signal79.701569
NoiseAvg:4.25,Std:0.18,Min:3.8,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.256893
#P14695
Spike_AFFX-r2-Bs-phe_M_signal30.163912
Corner-Avg:26051,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.833527
Spike_AFFX-r2-Ec-bioB_3_signal51.273739
Spike_AFFX-r2-Bs-lys_M_signal14.194950
Spike_AFFX-r2-P1-cre_3_signal3150.919922
Spike_AFFX-r2-Bs-lys_3-5-ratio1.625941
Spike_AFFX-r2-Bs-dap_M_signal149.675751
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.737127
Spike_AFFX-r2-Ec-bioB_avg-signal54.962467
Spike_AFFX-r2-Bs-thr_avg-signal41.187012
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal561.679810
Spike_AFFX-r2-Bs-phe_5_signal26.006693
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal837.892334
RawQ3.244661
Spike_AFFX-r2-Bs-lys_5_signal16.181583
Signal(A)3.261946
%A33.976326
Signal(All)137.908966
Corner+Avg:426,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal179.797699
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal35.506123
Spike_AFFX-r2-Ec-bioD_avg-signal699.786072
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.423500
Spike_AFFX-r2-Bs-lys_avg-signal18.895611
Spike_AFFX-r2-P1-cre_avg-signal2753.261230
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal58.182819
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal30.558908
Spike_AFFX-r2-Bs-dap_3_signal223.707932
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.491762
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal166.711472
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.310297
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.078496
Spike_AFFX-r2-Bs-thr_M_signal44.121315
Signal(P)212.015732
Spike_AFFX-r2-Bs-phe_3-5-ratio1.365269
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:21851,Count:9
Spike_AFFX-r2-P1-cre_5_signal2355.602783
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7750
Signal(M)13.293387
BackgroundAvg:81.81,Std:1.11,Min:79.0,Max:83.9
Spike_AFFX-r2-Ec-bioC_avg-signal173.254578
Spike_AFFX-r2-Bs-dap_avg-signal151.028412
Spike_AFFX-r2-Bs-dap_3-5-ratio2.806820
Spike_AFFX-r2-Ec-bioB_5_signal46.780136
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.282007
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-17_tga256_SA_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 ("Gatz_569-17_tga256_SA_Rep2_ATH1") was made from "" 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: Gatz_569-17_tga256_SA_Rep2_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 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:0.332021
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.938012
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.936101
Spike_AFFX-r2-Bs-dap_5_signal27.802608
NoiseAvg:2.94,Std:0.18,Min:2.4,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.172147
#P15263
Spike_AFFX-r2-Bs-phe_M_signal15.935708
Corner-Avg:11499,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal70.474396
Spike_AFFX-r2-Ec-bioB_3_signal54.310131
Spike_AFFX-r2-Bs-lys_M_signal5.456133
Spike_AFFX-r2-P1-cre_3_signal2243.575195
Spike_AFFX-r2-Bs-lys_3-5-ratio1.890049
Spike_AFFX-r2-Bs-dap_M_signal94.175583
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.180327
Spike_AFFX-r2-Ec-bioB_avg-signal60.933979
Spike_AFFX-r2-Bs-thr_avg-signal41.429077
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal479.725586
Spike_AFFX-r2-Bs-phe_5_signal19.964375
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal763.448975
RawQ2.662536
Spike_AFFX-r2-Bs-lys_5_signal13.796794
Signal(A)2.293139
%A31.850065
Signal(All)134.226212
Corner+Avg:194,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal183.164734
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.373133
Spike_AFFX-r2-Ec-bioD_avg-signal621.587280
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.913635
Spike_AFFX-r2-Bs-lys_avg-signal15.109848
Spike_AFFX-r2-P1-cre_avg-signal2317.708496
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.236300
Spike_AFFX-r2-Bs-thr_3_signal69.047523
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.424406
Spike_AFFX-r2-Bs-dap_3_signal133.138168
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.591429
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal179.916656
#M282
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.076616
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.018053
Spike_AFFX-r2-Bs-thr_M_signal44.067562
Signal(P)199.319824
Spike_AFFX-r2-Bs-phe_3-5-ratio0.970385
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8285,Count:9
Spike_AFFX-r2-P1-cre_5_signal2391.841553
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7265
Signal(M)10.005786
BackgroundAvg:62.92,Std:1.31,Min:59.5,Max:65.6
Spike_AFFX-r2-Ec-bioC_avg-signal181.540695
Spike_AFFX-r2-Bs-dap_avg-signal85.038788
Spike_AFFX-r2-Bs-dap_3-5-ratio4.788693
Spike_AFFX-r2-Ec-bioB_5_signal58.017403
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.332021
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-18_tga256_SA_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 ("Gatz_569-18_tga256_SA_Rep3_ATH1") was made from "" 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: Gatz_569-18_tga256_SA_Rep3_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 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:0.523747
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-ratio1.330131
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.816063
Spike_AFFX-r2-Bs-dap_5_signal105.145149
NoiseAvg:2.96,Std:0.14,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.272572
#P13846
Spike_AFFX-r2-Bs-phe_M_signal45.408588
Corner-Avg:19092,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.515015
Spike_AFFX-r2-Ec-bioB_3_signal67.435669
Spike_AFFX-r2-Bs-lys_M_signal20.629770
Spike_AFFX-r2-P1-cre_3_signal5177.806152
Spike_AFFX-r2-Bs-lys_3-5-ratio2.559615
Spike_AFFX-r2-Bs-dap_M_signal207.202103
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.110190
Spike_AFFX-r2-Ec-bioB_avg-signal82.195351
Spike_AFFX-r2-Bs-thr_avg-signal70.437836
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal984.128723
Spike_AFFX-r2-Bs-phe_5_signal48.155598
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1396.088867
RawQ2.592191
Spike_AFFX-r2-Bs-lys_5_signal23.582251
Signal(A)4.371333
%A37.531784
Signal(All)149.249908
Corner+Avg:312,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal304.662109
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.218510
Spike_AFFX-r2-Ec-bioD_avg-signal1190.108765
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.701447
Spike_AFFX-r2-Bs-lys_avg-signal34.857838
Spike_AFFX-r2-P1-cre_avg-signal4535.254883
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.766769
Spike_AFFX-r2-Bs-thr_3_signal97.263626
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal51.594234
Spike_AFFX-r2-Bs-dap_3_signal407.979492
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.418604
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal241.521378
#M403
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.361488
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.261429
Spike_AFFX-r2-Bs-thr_M_signal82.777313
Signal(P)242.705597
Spike_AFFX-r2-Bs-phe_3-5-ratio1.271265
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13659,Count:9
Spike_AFFX-r2-P1-cre_5_signal3892.703369
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8561
Signal(M)16.044004
BackgroundAvg:61.29,Std:0.71,Min:59.3,Max:63.1
Spike_AFFX-r2-Ec-bioC_avg-signal273.091736
Spike_AFFX-r2-Bs-dap_avg-signal240.108902
Spike_AFFX-r2-Bs-dap_3-5-ratio3.880155
Spike_AFFX-r2-Ec-bioB_5_signal82.635376
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.523747
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-19_tga256_ACC_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 ("Gatz_569-19_tga256_ACC_Rep1_ATH1") was made from "" 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: Gatz_569-19_tga256_ACC_Rep1_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC
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:0.488232
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-ratio1.372539
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.461912
Spike_AFFX-r2-Bs-dap_5_signal76.123520
NoiseAvg:3.59,Std:0.15,Min:3.3,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal33.822071
#P13996
Spike_AFFX-r2-Bs-phe_M_signal38.595417
Corner-Avg:23619,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.284630
Spike_AFFX-r2-Ec-bioB_3_signal70.245667
Spike_AFFX-r2-Bs-lys_M_signal18.202452
Spike_AFFX-r2-P1-cre_3_signal4128.688477
Spike_AFFX-r2-Bs-lys_3-5-ratio2.068829
Spike_AFFX-r2-Bs-dap_M_signal161.614136
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.123994
Spike_AFFX-r2-Ec-bioB_avg-signal70.193611
Spike_AFFX-r2-Bs-thr_avg-signal70.049232
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal796.778381
Spike_AFFX-r2-Bs-phe_5_signal30.973364
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1229.204102
RawQ3.061673
Spike_AFFX-r2-Bs-lys_5_signal19.110489
Signal(A)4.472992
%A36.909252
Signal(All)144.646515
Corner+Avg:406,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal232.744781
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.738087
Spike_AFFX-r2-Ec-bioD_avg-signal1012.991211
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.359055
Spike_AFFX-r2-Bs-lys_avg-signal25.616425
Spike_AFFX-r2-P1-cre_avg-signal3568.377441
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.731697
Spike_AFFX-r2-Bs-thr_3_signal105.659943
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-signal38.102291
Spike_AFFX-r2-Bs-dap_3_signal241.318054
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.542718
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal237.334900
#M395
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.536331
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.980660
Spike_AFFX-r2-Bs-thr_M_signal70.665695
Signal(P)232.584579
Spike_AFFX-r2-Bs-phe_3-5-ratio1.444405
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:17101,Count:9
Spike_AFFX-r2-P1-cre_5_signal3008.066406
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8419
Signal(M)16.393160
BackgroundAvg:74.58,Std:0.31,Min:73.6,Max:75.6
Spike_AFFX-r2-Ec-bioC_avg-signal235.039841
Spike_AFFX-r2-Bs-dap_avg-signal159.685242
Spike_AFFX-r2-Bs-dap_3-5-ratio3.170085
Spike_AFFX-r2-Ec-bioB_5_signal48.050533
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.488232
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-20_tga256_ACC_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 ("Gatz_569-20_tga256_ACC_Rep2_ATH1") was made from "" 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: Gatz_569-20_tga256_ACC_Rep2_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC
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:0.255386
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-ratio1.346058
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.031153
Spike_AFFX-r2-Bs-dap_5_signal35.419460
NoiseAvg:3.03,Std:0.09,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.835233
#P15591
Spike_AFFX-r2-Bs-phe_M_signal16.000626
Corner-Avg:11804,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal64.505051
Spike_AFFX-r2-Ec-bioB_3_signal50.481205
Spike_AFFX-r2-Bs-lys_M_signal4.240496
Spike_AFFX-r2-P1-cre_3_signal2749.728271
Spike_AFFX-r2-Bs-lys_3-5-ratio1.884567
Spike_AFFX-r2-Bs-dap_M_signal93.183609
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.092718
Spike_AFFX-r2-Ec-bioB_avg-signal54.647434
Spike_AFFX-r2-Bs-thr_avg-signal26.985727
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal455.765594
Spike_AFFX-r2-Bs-phe_5_signal16.175043
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal694.093628
RawQ2.643631
Spike_AFFX-r2-Bs-lys_5_signal9.818430
Signal(A)1.826413
%A30.416485
Signal(All)132.002472
Corner+Avg:189,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal177.225342
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.330141
Spike_AFFX-r2-Ec-bioD_avg-signal574.929626
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.351601
Spike_AFFX-r2-Bs-lys_avg-signal10.854138
Spike_AFFX-r2-P1-cre_avg-signal2396.264648
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.231916
Spike_AFFX-r2-Bs-thr_3_signal33.138683
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.168602
Spike_AFFX-r2-Bs-dap_3_signal134.689240
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.522918
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal154.366165
#M281
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.503490
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.148084
Spike_AFFX-r2-Bs-thr_M_signal31.983265
Signal(P)192.158890
Spike_AFFX-r2-Bs-phe_3-5-ratio1.380531
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9735,Count:9
Spike_AFFX-r2-P1-cre_5_signal2042.800781
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6938
Signal(M)8.382650
BackgroundAvg:62.38,Std:0.55,Min:60.8,Max:64.1
Spike_AFFX-r2-Ec-bioC_avg-signal165.795746
Spike_AFFX-r2-Bs-dap_avg-signal87.764099
Spike_AFFX-r2-Bs-dap_3-5-ratio3.802690
Spike_AFFX-r2-Ec-bioB_5_signal48.956059
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.255386
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-21_tga256_ACC_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 ("Gatz_569-21_tga256_ACC_Rep3_ATH1") was made from "" 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: Gatz_569-21_tga256_ACC_Rep3_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Growth Conditions:
Stratification2 days at 4°C in the dark
ProtocolPlants grown for 4 weeks in soil (21/19°C, 16-h light/8-h dark cycle, 60% relative humidity)
Substrate Sterilising ProcedureARCHUT, Fruhstorfer Erde
Plant Spacingone plant per pot
waterevery 4 days
Temperature21 °C average, 21 °C day, 19 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC
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:0.939116
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-ratio1.302924
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.039607
Spike_AFFX-r2-Bs-dap_5_signal226.026230
NoiseAvg:2.46,Std:0.12,Min:2.1,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_signal63.708775
#P13521
Spike_AFFX-r2-Bs-phe_M_signal64.845810
Corner-Avg:18499,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal188.140167
Spike_AFFX-r2-Ec-bioB_3_signal146.087128
Spike_AFFX-r2-Bs-lys_M_signal37.958584
Spike_AFFX-r2-P1-cre_3_signal9427.806641
Spike_AFFX-r2-Bs-lys_3-5-ratio1.519620
Spike_AFFX-r2-Bs-dap_M_signal400.274811
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.716014
Spike_AFFX-r2-Ec-bioB_avg-signal158.249619
Spike_AFFX-r2-Bs-thr_avg-signal127.827644
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1957.640747
Spike_AFFX-r2-Bs-phe_5_signal102.164856
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2637.509766
RawQ2.440162
Spike_AFFX-r2-Bs-lys_5_signal39.997383
Signal(A)5.543775
%A38.772469
Signal(All)152.241196
Corner+Avg:289,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal574.998657
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal86.905861
Spike_AFFX-r2-Ec-bioD_avg-signal2297.575195
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.276634
Spike_AFFX-r2-Bs-lys_avg-signal46.245594
Spike_AFFX-r2-P1-cre_avg-signal8331.844727
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.950899
Spike_AFFX-r2-Bs-thr_3_signal173.033905
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-signal84.638847
Spike_AFFX-r2-Bs-dap_3_signal671.445190
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.347290
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal416.603729
#M445
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.780827
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.380205
Spike_AFFX-r2-Bs-thr_M_signal146.740280
Signal(P)252.565674
Spike_AFFX-r2-Bs-phe_3-5-ratio0.850643
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16028,Count:9
Spike_AFFX-r2-P1-cre_5_signal7235.883301
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8844
Signal(M)19.442863
BackgroundAvg:54.09,Std:0.93,Min:51.3,Max:55.7
Spike_AFFX-r2-Ec-bioC_avg-signal495.801208
Spike_AFFX-r2-Bs-dap_avg-signal432.582062
Spike_AFFX-r2-Bs-dap_3-5-ratio2.970652
Spike_AFFX-r2-Ec-bioB_5_signal140.521530
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.939116
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-22_tga256 SA+ACC_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 ("Gatz_569-22_tga256 SA+ACC_Rep1_ATH1") was made from "" 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: Gatz_569-22_tga256 SA+ACC_Rep1_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC and 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:0.277677
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-ratio1.401982
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.145817
Spike_AFFX-r2-Bs-dap_5_signal73.130501
NoiseAvg:4.09,Std:0.13,Min:3.8,Max:4.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.196064
#P14802
Spike_AFFX-r2-Bs-phe_M_signal21.452156
Corner-Avg:28459,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.221367
Spike_AFFX-r2-Ec-bioB_3_signal59.892994
Spike_AFFX-r2-Bs-lys_M_signal9.991879
Spike_AFFX-r2-P1-cre_3_signal3198.067627
Spike_AFFX-r2-Bs-lys_3-5-ratio1.543603
Spike_AFFX-r2-Bs-dap_M_signal133.959061
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.166870
Spike_AFFX-r2-Ec-bioB_avg-signal62.128460
Spike_AFFX-r2-Bs-thr_avg-signal42.007401
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal663.426208
Spike_AFFX-r2-Bs-phe_5_signal34.864037
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal922.408875
RawQ3.224332
Spike_AFFX-r2-Bs-lys_5_signal16.390295
Signal(A)2.817937
%A33.643139
Signal(All)136.145096
Corner+Avg:475,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal200.102249
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.948879
Spike_AFFX-r2-Ec-bioD_avg-signal792.917542
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.892593
Spike_AFFX-r2-Bs-lys_avg-signal17.227427
Spike_AFFX-r2-P1-cre_avg-signal2739.586182
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.464270
Spike_AFFX-r2-Bs-thr_3_signal54.596588
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal29.755026
Spike_AFFX-r2-Bs-dap_3_signal237.603867
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.390371
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal173.949341
#M334
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.300108
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.150348
Spike_AFFX-r2-Bs-thr_M_signal46.229553
Signal(P)208.073517
Spike_AFFX-r2-Bs-phe_3-5-ratio0.945068
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:22529,Count:9
Spike_AFFX-r2-P1-cre_5_signal2281.104736
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7674
Signal(M)11.798442
BackgroundAvg:76.28,Std:0.86,Min:74.2,Max:78.8
Spike_AFFX-r2-Ec-bioC_avg-signal187.025787
Spike_AFFX-r2-Bs-dap_avg-signal148.231140
Spike_AFFX-r2-Bs-dap_3-5-ratio3.249039
Spike_AFFX-r2-Ec-bioB_5_signal52.271008
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.277677
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-23_tga256 SA+ACC_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Gatz_569-23_tga256 SA+ACC_Rep2_ATH1") was made from "" 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: Gatz_569-23_tga256 SA+ACC_Rep2_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC and 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:0.299634
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-ratio1.267086
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.795214
Spike_AFFX-r2-Bs-dap_5_signal31.939589
NoiseAvg:2.83,Std:0.09,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.406409
#P15502
Spike_AFFX-r2-Bs-phe_M_signal14.984097
Corner-Avg:10241,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.998138
Spike_AFFX-r2-Ec-bioB_3_signal49.861481
Spike_AFFX-r2-Bs-lys_M_signal6.822767
Spike_AFFX-r2-P1-cre_3_signal3091.227295
Spike_AFFX-r2-Bs-lys_3-5-ratio1.869517
Spike_AFFX-r2-Bs-dap_M_signal91.319382
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.864519
Spike_AFFX-r2-Ec-bioB_avg-signal65.187187
Spike_AFFX-r2-Bs-thr_avg-signal27.481552
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal462.789459
Spike_AFFX-r2-Bs-phe_5_signal16.092339
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal794.398376
RawQ2.439576
Spike_AFFX-r2-Bs-lys_5_signal9.599656
Signal(A)2.004052
%A30.898729
Signal(All)132.835159
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal186.960083
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.699295
Spike_AFFX-r2-Ec-bioD_avg-signal628.593933
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.961418
Spike_AFFX-r2-Bs-lys_avg-signal11.456382
Spike_AFFX-r2-P1-cre_avg-signal2765.431152
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.139851
Spike_AFFX-r2-Bs-thr_3_signal38.402912
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.925243
Spike_AFFX-r2-Bs-dap_3_signal127.804222
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.716544
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal191.436905
#M260
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.946722
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.976615
Spike_AFFX-r2-Bs-thr_M_signal30.635334
Signal(P)194.396027
Spike_AFFX-r2-Bs-phe_3-5-ratio1.410565
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7904,Count:9
Spike_AFFX-r2-P1-cre_5_signal2439.634766
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7048
Signal(M)8.916574
BackgroundAvg:56.55,Std:0.53,Min:55.0,Max:57.6
Spike_AFFX-r2-Ec-bioC_avg-signal189.198486
Spike_AFFX-r2-Bs-dap_avg-signal83.687729
Spike_AFFX-r2-Bs-dap_3-5-ratio4.001436
Spike_AFFX-r2-Ec-bioB_5_signal62.701946
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.299634
NF1.000000
HZ4
Tau0.015000

Slide: Gatz_569-24_tga256 SA+ACC_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 ("Gatz_569-24_tga256 SA+ACC_Rep3_ATH1") was made from "" 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: Gatz_569-24_tga256 SA+ACC_Rep3_ATH1
Organism:
Alias: tga256
Stock Code:
Genetic Background: Col
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Genetic Variation: At5g06950
Tissue: above-ground rosette
in vivo Treatment: Plants treated for 12h with 1mM ACC and 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:0.367874
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-ratio1.244299
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.719106
Spike_AFFX-r2-Bs-dap_5_signal29.601814
NoiseAvg:2.73,Std:0.07,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.635751
#P15329
Spike_AFFX-r2-Bs-phe_M_signal18.274246
Corner-Avg:10727,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.611366
Spike_AFFX-r2-Ec-bioB_3_signal48.174122
Spike_AFFX-r2-Bs-lys_M_signal3.795534
Spike_AFFX-r2-P1-cre_3_signal3171.678955
Spike_AFFX-r2-Bs-lys_3-5-ratio1.712239
Spike_AFFX-r2-Bs-dap_M_signal84.422195
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.144535
Spike_AFFX-r2-Ec-bioB_avg-signal65.259056
Spike_AFFX-r2-Bs-thr_avg-signal23.911829
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal489.650574
Spike_AFFX-r2-Bs-phe_5_signal13.729187
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal780.148987
RawQ2.438920
Spike_AFFX-r2-Bs-lys_5_signal12.584382
Signal(A)2.266724
%A31.486191
Signal(All)134.758270
Corner+Avg:176,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal229.151428
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.859770
Spike_AFFX-r2-Ec-bioD_avg-signal634.899780
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.202980
Spike_AFFX-r2-Bs-lys_avg-signal12.642460
Spike_AFFX-r2-P1-cre_avg-signal2860.323730
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.310829
Spike_AFFX-r2-Bs-thr_3_signal33.444492
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.954401
Spike_AFFX-r2-Bs-dap_3_signal142.818970
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.593277
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal176.965607
#M299
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.547464
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.294892
Spike_AFFX-r2-Bs-thr_M_signal27.655245
Signal(P)199.271393
Spike_AFFX-r2-Bs-phe_3-5-ratio1.592211
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7547,Count:9
Spike_AFFX-r2-P1-cre_5_signal2548.968262
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7182
Signal(M)9.783038
BackgroundAvg:57.77,Std:0.50,Min:56.4,Max:59.2
Spike_AFFX-r2-Ec-bioC_avg-signal203.058517
Spike_AFFX-r2-Bs-dap_avg-signal85.614326
Spike_AFFX-r2-Bs-dap_3-5-ratio4.824669
Spike_AFFX-r2-Ec-bioB_5_signal66.991669
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.367874
NF1.000000
HZ4
Tau0.015000


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