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Experiment: Compatibility to Downy Mildew (Hyaloperonospora arabidopsidis) infection

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-585

The analysis of physiological and molecular determinants accounting for successful infection by pathogenic oomycetes has become a topic of prime scientific interest during the last years. The hunt is now on for pathogen effectors subverting the host cell, and for the plant compatibility functions manipulated by these effectors. An understanding of the molecular mechanisms underlying successful infection should make it possible to develop new crop protection strategies based on interference with compatibility to prevent disease. We identified several Arabidopsis genes that account for full susceptibility to the Downy Mildew pathogen, Hyaloperonospora arabidopsidis. A common denominator is that mutants, in which these genes were knocked-out, are more resistant (= less susceptible) to infection. Here, we aim at analyzing the metabolic pathways that are responsible for the lowered susceptibility phenotype of three mutant lines, which are deficient for a microtubule-associated protein (MAP65-3), a leucine-rich repeat receptor-like kinase (PSKR1), and a glycosyltransferase.The Wassilewskija (Ws-4) wild-typ and the mutant lines dyc283, eyw110, and egy19 were from the T-DNA insertion collection at INRA, Versailles, France. Seeds were sown to high density on a soil/sand mixture in 6 cm x 6 cm pots, stratified for 3 days at 4 °C, and then grown under a 16 h photoperiod in a growth chamber at 20 °C. For control treatment and infection, 8-day-old plants were spray-inoculated to saturation with either water, or a H. arabidopsidis isolate Emwa1 spore suspension at 40,000 spores/ml, respectively. Plants were kept in a growth cabinet at 16°C for 3 d with a 16 h photoperiod, before the aerial parts including hypocotyls, fully expanded cotyledons, and leaf primordia were pooled from ~500 plantlets for RNA extraction.

About the Experimenter

Name:Dr Harald Keller
Head of Lab Name:Dr Harald Keller
Lab:
Institute: Equipe Interactions Plantes-Oomycetes, UMR Interactions Biotiques et Santale, Institut National de la Recherche Agronomique (INRA)
Address:
400, Route des Chappes. Boïte Postale 167 , Sophia-Antipolis Cedex, Antibes, Alpes-Maritimes
Postcode: 06903
Country: FRANCE
 
Telephone Number: 33(0)4 92 38 65 94
Fax Number: 33(0)4 92 38 65 87

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

About this Experiment

Experiment Type: genetic_modification_design
Number of Slides:16
 
Experimental Parameters:
parameterinfect
parametergene_knock_out
parameter
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Keller: Compatibility to Downy Mildew (Hyaloperonospora arabidopsidis) infection

Slide: Keller_585-1_Ws_Water_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 ("Keller_585-1_Ws_Water_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: Keller_585-1_Ws_Water_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Ws-4 (Wassilewskija) (INRA)
Stock Code: N5390
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.482859
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-ratio1.300662
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.114708
Spike_AFFX-r2-Bs-dap_5_signal78.495010
NoiseAvg:3.29,Std:0.14,Min:3.0,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_signal33.131245
#P14487
Spike_AFFX-r2-Bs-phe_M_signal58.859715
Corner-Avg:11881,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal118.323868
Spike_AFFX-r2-Ec-bioB_3_signal85.842339
Spike_AFFX-r2-Bs-lys_M_signal10.657622
Spike_AFFX-r2-P1-cre_3_signal4679.899414
Spike_AFFX-r2-Bs-lys_3-5-ratio0.878876
Spike_AFFX-r2-Bs-dap_M_signal217.509796
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.917024
Spike_AFFX-r2-Ec-bioB_avg-signal93.725006
Spike_AFFX-r2-Bs-thr_avg-signal80.223854
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal872.626526
Spike_AFFX-r2-Bs-phe_5_signal43.172646
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1450.017944
RawQ2.860266
Spike_AFFX-r2-Bs-lys_5_signal30.391106
Signal(A)4.553260
%A34.305130
Signal(All)151.975998
Corner+Avg:193,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal317.889587
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal47.942825
Spike_AFFX-r2-Ec-bioD_avg-signal1161.322266
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.511620
Spike_AFFX-r2-Bs-lys_avg-signal22.586245
Spike_AFFX-r2-P1-cre_avg-signal4138.995117
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.183253
Spike_AFFX-r2-Bs-thr_3_signal129.775894
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-signal49.991730
Spike_AFFX-r2-Bs-dap_3_signal224.651001
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.661671
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal376.242035
#M498
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.710007
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.844907
Spike_AFFX-r2-Bs-thr_M_signal77.764420
Signal(P)236.314590
Spike_AFFX-r2-Bs-phe_3-5-ratio1.110491
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9750,Count:9
Spike_AFFX-r2-P1-cre_5_signal3598.091309
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7825
Signal(M)14.967202
BackgroundAvg:67.23,Std:0.34,Min:66.3,Max:68.1
Spike_AFFX-r2-Ec-bioC_avg-signal347.065796
Spike_AFFX-r2-Bs-dap_avg-signal173.551941
Spike_AFFX-r2-Bs-dap_3-5-ratio2.861978
Spike_AFFX-r2-Ec-bioB_5_signal77.008812
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.482859
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-2_Ws_Water_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 ("Keller_585-2_Ws_Water_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: Keller_585-2_Ws_Water_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Ws-4 (Wassilewskija) (INRA)
Stock Code: N5390
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.403699
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-ratio1.202227
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.287155
Spike_AFFX-r2-Bs-dap_5_signal56.178741
NoiseAvg:3.12,Std:0.08,Min:2.9,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal38.003857
#P14613
Spike_AFFX-r2-Bs-phe_M_signal51.470779
Corner-Avg:10879,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal100.693321
Spike_AFFX-r2-Ec-bioB_3_signal79.365410
Spike_AFFX-r2-Bs-lys_M_signal14.229197
Spike_AFFX-r2-P1-cre_3_signal3843.761475
Spike_AFFX-r2-Bs-lys_3-5-ratio1.528169
Spike_AFFX-r2-Bs-dap_M_signal234.676682
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.177489
Spike_AFFX-r2-Ec-bioB_avg-signal80.572769
Spike_AFFX-r2-Bs-thr_avg-signal82.033394
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal883.317261
Spike_AFFX-r2-Bs-phe_5_signal41.519867
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1228.010986
RawQ2.804658
Spike_AFFX-r2-Bs-lys_5_signal25.560549
Signal(A)3.539008
%A34.024551
Signal(All)149.730072
Corner+Avg:183,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal294.796387
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.520798
Spike_AFFX-r2-Ec-bioD_avg-signal1055.664063
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.064011
Spike_AFFX-r2-Bs-lys_avg-signal26.283525
Spike_AFFX-r2-P1-cre_avg-signal3520.480713
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.911442
Spike_AFFX-r2-Bs-thr_3_signal120.756836
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-signal48.503815
Spike_AFFX-r2-Bs-dap_3_signal274.037811
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.390226
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal300.013885
#M436
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.060833
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.982609
Spike_AFFX-r2-Bs-thr_M_signal87.339478
Signal(P)231.422501
Spike_AFFX-r2-Bs-phe_3-5-ratio1.264956
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8553,Count:9
Spike_AFFX-r2-P1-cre_5_signal3197.199951
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7761
Signal(M)13.990530
BackgroundAvg:65.71,Std:0.42,Min:64.6,Max:67.0
Spike_AFFX-r2-Ec-bioC_avg-signal297.405151
Spike_AFFX-r2-Bs-dap_avg-signal188.297729
Spike_AFFX-r2-Bs-dap_3-5-ratio4.877963
Spike_AFFX-r2-Ec-bioB_5_signal61.659580
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.403699
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-3_Ws_Ha_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 ("Keller_585-3_Ws_Ha_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: Keller_585-3_Ws_Ha_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Ws-4 (Wassilewskija) (INRA)
Stock Code: N5390
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.511655
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-ratio1.189869
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.949962
Spike_AFFX-r2-Bs-dap_5_signal39.794964
NoiseAvg:3.17,Std:0.34,Min:2.6,Max:5.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.841318
#P14665
Spike_AFFX-r2-Bs-phe_M_signal34.873596
Corner-Avg:10813,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.699554
Spike_AFFX-r2-Ec-bioB_3_signal78.645638
Spike_AFFX-r2-Bs-lys_M_signal16.090647
Spike_AFFX-r2-P1-cre_3_signal4516.037598
Spike_AFFX-r2-Bs-lys_3-5-ratio2.294863
Spike_AFFX-r2-Bs-dap_M_signal168.636948
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.236878
Spike_AFFX-r2-Ec-bioB_avg-signal87.044456
Spike_AFFX-r2-Bs-thr_avg-signal83.731529
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal867.187256
Spike_AFFX-r2-Bs-phe_5_signal41.343880
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1167.154663
RawQ2.683382
Spike_AFFX-r2-Bs-lys_5_signal27.074114
Signal(A)4.241111
%A33.678211
Signal(All)150.117966
Corner+Avg:187,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal365.663574
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.220737
Spike_AFFX-r2-Ec-bioD_avg-signal1017.170959
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.291977
Spike_AFFX-r2-Bs-lys_avg-signal35.098713
Spike_AFFX-r2-P1-cre_avg-signal4155.722168
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.029811
Spike_AFFX-r2-Bs-thr_3_signal135.327835
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-signal40.146069
Spike_AFFX-r2-Bs-dap_3_signal268.011444
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.345908
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal347.865997
#M463
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal62.131386
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.051162
Spike_AFFX-r2-Bs-thr_M_signal90.025429
Signal(P)230.766037
Spike_AFFX-r2-Bs-phe_3-5-ratio1.069584
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8422,Count:9
Spike_AFFX-r2-P1-cre_5_signal3795.406494
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7682
Signal(M)16.040089
BackgroundAvg:65.50,Std:0.74,Min:64.0,Max:68.5
Spike_AFFX-r2-Ec-bioC_avg-signal356.764771
Spike_AFFX-r2-Bs-dap_avg-signal158.814438
Spike_AFFX-r2-Bs-dap_3-5-ratio6.734808
Spike_AFFX-r2-Ec-bioB_5_signal82.788177
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.511655
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-4_Ws_Ha_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 ("Keller_585-4_Ws_Ha_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: Keller_585-4_Ws_Ha_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Ws-4 (Wassilewskija) (INRA)
Stock Code: N5390
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.523724
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-ratio1.173425
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.002328
Spike_AFFX-r2-Bs-dap_5_signal38.600086
NoiseAvg:3.29,Std:0.09,Min:2.9,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_signal16.225227
#P14217
Spike_AFFX-r2-Bs-phe_M_signal17.940163
Corner-Avg:10566,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal72.807976
Spike_AFFX-r2-Ec-bioB_3_signal58.666458
Spike_AFFX-r2-Bs-lys_M_signal7.391239
Spike_AFFX-r2-P1-cre_3_signal4038.595947
Spike_AFFX-r2-Bs-lys_3-5-ratio2.191328
Spike_AFFX-r2-Bs-dap_M_signal107.283623
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.565161
Spike_AFFX-r2-Ec-bioB_avg-signal63.334869
Spike_AFFX-r2-Bs-thr_avg-signal43.797302
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal688.124146
Spike_AFFX-r2-Bs-phe_5_signal22.697969
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1118.242920
RawQ3.019648
Spike_AFFX-r2-Bs-lys_5_signal14.626237
Signal(A)4.881524
%A35.493206
Signal(All)150.497971
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal304.555573
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.794209
Spike_AFFX-r2-Ec-bioD_avg-signal903.183533
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.327927
Spike_AFFX-r2-Bs-lys_avg-signal18.022785
Spike_AFFX-r2-P1-cre_avg-signal3740.156494
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.178869
Spike_AFFX-r2-Bs-thr_3_signal74.070778
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.144114
Spike_AFFX-r2-Bs-dap_3_signal168.706497
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.625060
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal279.307129
#M497
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.050880
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.090397
Spike_AFFX-r2-Bs-thr_M_signal41.095890
Signal(P)238.129944
Spike_AFFX-r2-Bs-phe_3-5-ratio1.532922
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8447,Count:9
Spike_AFFX-r2-P1-cre_5_signal3441.717041
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8096
Signal(M)15.783384
BackgroundAvg:73.91,Std:0.42,Min:72.8,Max:75.1
Spike_AFFX-r2-Ec-bioC_avg-signal291.931335
Spike_AFFX-r2-Bs-dap_avg-signal104.863403
Spike_AFFX-r2-Bs-dap_3-5-ratio4.370625
Spike_AFFX-r2-Ec-bioB_5_signal58.530190
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.523724
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-5_dyc283_Water_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 ("Keller_585-5_dyc283_Water_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: Keller_585-5_dyc283_Water_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: DYC
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At5g51600
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.568469
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-ratio1.282588
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.139741
Spike_AFFX-r2-Bs-dap_5_signal70.297684
NoiseAvg:2.90,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_signal43.127537
#P14367
Spike_AFFX-r2-Bs-phe_M_signal39.737988
Corner-Avg:10708,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal133.402374
Spike_AFFX-r2-Ec-bioB_3_signal102.362663
Spike_AFFX-r2-Bs-lys_M_signal22.281322
Spike_AFFX-r2-P1-cre_3_signal4957.507813
Spike_AFFX-r2-Bs-lys_3-5-ratio1.835584
Spike_AFFX-r2-Bs-dap_M_signal222.272797
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.604669
Spike_AFFX-r2-Ec-bioB_avg-signal108.525749
Spike_AFFX-r2-Bs-thr_avg-signal89.210846
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1060.724976
Spike_AFFX-r2-Bs-phe_5_signal41.977074
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1649.382202
RawQ2.868376
Spike_AFFX-r2-Bs-lys_5_signal22.817751
Signal(A)4.454704
%A35.019730
Signal(All)155.889206
Corner+Avg:169,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal389.334961
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal43.865170
Spike_AFFX-r2-Ec-bioD_avg-signal1355.053589
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.985531
Spike_AFFX-r2-Bs-lys_avg-signal28.994318
Spike_AFFX-r2-P1-cre_avg-signal4411.372070
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.994739
Spike_AFFX-r2-Bs-thr_3_signal112.332970
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-signal41.860077
Spike_AFFX-r2-Bs-dap_3_signal228.041260
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.554957
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal384.841278
#M455
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.883888
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.011677
Spike_AFFX-r2-Bs-thr_M_signal112.172028
Signal(P)244.524628
Spike_AFFX-r2-Bs-phe_3-5-ratio1.044979
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9301,Count:9
Spike_AFFX-r2-P1-cre_5_signal3865.236572
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7988
Signal(M)15.744016
BackgroundAvg:66.37,Std:0.60,Min:64.5,Max:67.8
Spike_AFFX-r2-Ec-bioC_avg-signal387.088135
Spike_AFFX-r2-Bs-dap_avg-signal173.537247
Spike_AFFX-r2-Bs-dap_3-5-ratio3.243937
Spike_AFFX-r2-Ec-bioB_5_signal89.812187
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.568469
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-6_dyc283_Water_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 ("Keller_585-6_dyc283_Water_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: Keller_585-6_dyc283_Water_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: DYC
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At5g51600
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.81136
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-ratio1.094748
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.175652
Spike_AFFX-r2-Bs-dap_5_signal44.038239
NoiseAvg:2.98,Std:0.12,Min:2.7,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_signal20.455387
#P13387
Spike_AFFX-r2-Bs-phe_M_signal23.602644
Corner-Avg:9683,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal100.945198
Spike_AFFX-r2-Ec-bioB_3_signal76.819374
Spike_AFFX-r2-Bs-lys_M_signal20.838570
Spike_AFFX-r2-P1-cre_3_signal3961.917725
Spike_AFFX-r2-Bs-lys_3-5-ratio1.541241
Spike_AFFX-r2-Bs-dap_M_signal129.123154
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.082862
Spike_AFFX-r2-Ec-bioB_avg-signal81.035500
Spike_AFFX-r2-Bs-thr_avg-signal64.275909
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal945.332825
Spike_AFFX-r2-Bs-phe_5_signal44.256779
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1266.803467
RawQ2.915112
Spike_AFFX-r2-Bs-lys_5_signal14.424131
Signal(A)6.077676
%A39.083736
Signal(All)159.567169
Corner+Avg:157,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal269.308685
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal35.208561
Spike_AFFX-r2-Ec-bioD_avg-signal1106.068115
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.689171
Spike_AFFX-r2-Bs-lys_avg-signal19.164589
Spike_AFFX-r2-P1-cre_avg-signal3790.469727
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.227093
Spike_AFFX-r2-Bs-thr_3_signal103.971909
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-signal34.355991
Spike_AFFX-r2-Bs-dap_3_signal171.461884
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.340061
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal338.889099
#M508
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.231064
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.794681
Spike_AFFX-r2-Bs-thr_M_signal68.400436
Signal(P)266.988556
Spike_AFFX-r2-Bs-phe_3-5-ratio0.795552
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7863,Count:9
Spike_AFFX-r2-P1-cre_5_signal3619.021973
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8915
Signal(M)22.379509
BackgroundAvg:70.87,Std:1.20,Min:67.1,Max:73.0
Spike_AFFX-r2-Ec-bioC_avg-signal304.098877
Spike_AFFX-r2-Bs-dap_avg-signal114.874420
Spike_AFFX-r2-Bs-dap_3-5-ratio3.893477
Spike_AFFX-r2-Ec-bioB_5_signal65.341919
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.811360
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-7_dyc283_Ha_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 ("Keller_585-7_dyc283_Ha_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: Keller_585-7_dyc283_Ha_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: DYC
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At5g51600
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.593374
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-ratio1.024779
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.040416
Spike_AFFX-r2-Bs-dap_5_signal49.066704
NoiseAvg:3.58,Std:0.12,Min:3.3,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.880764
#P13906
Spike_AFFX-r2-Bs-phe_M_signal30.002621
Corner-Avg:10993,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.526108
Spike_AFFX-r2-Ec-bioB_3_signal68.044380
Spike_AFFX-r2-Bs-lys_M_signal11.017042
Spike_AFFX-r2-P1-cre_3_signal3674.459717
Spike_AFFX-r2-Bs-lys_3-5-ratio1.603514
Spike_AFFX-r2-Bs-dap_M_signal114.037819
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.385781
Spike_AFFX-r2-Ec-bioB_avg-signal71.990547
Spike_AFFX-r2-Bs-thr_avg-signal61.971882
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal852.437378
Spike_AFFX-r2-Bs-phe_5_signal29.604916
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1147.427124
RawQ3.305691
Spike_AFFX-r2-Bs-lys_5_signal20.534317
Signal(A)5.869801
%A36.878563
Signal(All)151.120651
Corner+Avg:194,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal244.984009
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.877750
Spike_AFFX-r2-Ec-bioD_avg-signal999.932251
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.964489
Spike_AFFX-r2-Bs-lys_avg-signal21.492807
Spike_AFFX-r2-P1-cre_avg-signal3630.036133
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.156949
Spike_AFFX-r2-Bs-thr_3_signal84.240814
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.161764
Spike_AFFX-r2-Bs-dap_3_signal191.494995
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.346054
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal272.756744
#M492
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.927063
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.898178
Spike_AFFX-r2-Bs-thr_M_signal76.794075
Signal(P)243.577621
Spike_AFFX-r2-Bs-phe_3-5-ratio1.144329
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8134,Count:9
Spike_AFFX-r2-P1-cre_5_signal3585.612305
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8412
Signal(M)21.331135
BackgroundAvg:82.99,Std:1.40,Min:78.2,Max:85.7
Spike_AFFX-r2-Ec-bioC_avg-signal258.870361
Spike_AFFX-r2-Bs-dap_avg-signal118.199837
Spike_AFFX-r2-Bs-dap_3-5-ratio3.902748
Spike_AFFX-r2-Ec-bioB_5_signal65.401154
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.593374
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-8_dyc283_Ha_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 ("Keller_585-8_dyc283_Ha_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: Keller_585-8_dyc283_Ha_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: DYC
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At5g51600
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.521754
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-ratio1.091424
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.782136
Spike_AFFX-r2-Bs-dap_5_signal79.656502
NoiseAvg:2.76,Std:0.10,Min:2.5,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_signal36.363468
#P14604
Spike_AFFX-r2-Bs-phe_M_signal55.665791
Corner-Avg:11741,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.895157
Spike_AFFX-r2-Ec-bioB_3_signal71.951317
Spike_AFFX-r2-Bs-lys_M_signal22.546419
Spike_AFFX-r2-P1-cre_3_signal4143.354980
Spike_AFFX-r2-Bs-lys_3-5-ratio1.835590
Spike_AFFX-r2-Bs-dap_M_signal267.716431
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.521966
Spike_AFFX-r2-Ec-bioB_avg-signal86.946617
Spike_AFFX-r2-Bs-thr_avg-signal88.050476
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal912.320557
Spike_AFFX-r2-Bs-phe_5_signal59.313652
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1276.287476
RawQ2.570522
Spike_AFFX-r2-Bs-lys_5_signal27.351025
Signal(A)4.358709
%A33.901798
Signal(All)150.646271
Corner+Avg:196,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal479.573883
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.359085
Spike_AFFX-r2-Ec-bioD_avg-signal1094.303955
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.024551
Spike_AFFX-r2-Bs-lys_avg-signal33.367569
Spike_AFFX-r2-P1-cre_avg-signal3969.818604
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.073652
Spike_AFFX-r2-Bs-thr_3_signal128.070892
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal55.112843
Spike_AFFX-r2-Bs-dap_3_signal363.839752
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.398946
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal318.571564
#M473
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.205257
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.505388
Spike_AFFX-r2-Bs-thr_M_signal99.717079
Signal(P)232.464874
Spike_AFFX-r2-Bs-phe_3-5-ratio0.849030
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9129,Count:9
Spike_AFFX-r2-P1-cre_5_signal3796.282227
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7733
Signal(M)16.107000
BackgroundAvg:59.49,Std:1.06,Min:56.2,Max:61.9
Spike_AFFX-r2-Ec-bioC_avg-signal399.072723
Spike_AFFX-r2-Bs-dap_avg-signal237.070877
Spike_AFFX-r2-Bs-dap_3-5-ratio4.567609
Spike_AFFX-r2-Ec-bioB_5_signal91.993378
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.521754
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-9_eyw110_Water_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 ("Keller_585-9_eyw110_Water_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: Keller_585-9_eyw110_Water_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At2g02220
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.561511
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-ratio1.223094
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.721583
Spike_AFFX-r2-Bs-dap_5_signal59.118900
NoiseAvg:3.21,Std:0.09,Min:3.0,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.702295
#P14120
Spike_AFFX-r2-Bs-phe_M_signal30.930496
Corner-Avg:10445,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal101.989975
Spike_AFFX-r2-Ec-bioB_3_signal52.570087
Spike_AFFX-r2-Bs-lys_M_signal10.045199
Spike_AFFX-r2-P1-cre_3_signal4174.670410
Spike_AFFX-r2-Bs-lys_3-5-ratio1.609830
Spike_AFFX-r2-Bs-dap_M_signal171.258804
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.619980
Spike_AFFX-r2-Ec-bioB_avg-signal75.804634
Spike_AFFX-r2-Bs-thr_avg-signal56.854160
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal795.593140
Spike_AFFX-r2-Bs-phe_5_signal25.434702
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1127.691772
RawQ3.068658
Spike_AFFX-r2-Bs-lys_5_signal14.601573
Signal(A)4.412913
%A36.181499
Signal(All)153.008789
Corner+Avg:166,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal301.079010
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.474318
Spike_AFFX-r2-Ec-bioD_avg-signal961.642456
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.902676
Spike_AFFX-r2-Bs-lys_avg-signal16.050943
Spike_AFFX-r2-P1-cre_avg-signal3793.937988
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.915826
Spike_AFFX-r2-Bs-thr_3_signal80.439407
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-signal29.279839
Spike_AFFX-r2-Bs-dap_3_signal169.092896
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.417423
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal284.090057
#M437
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.506056
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.059801
Spike_AFFX-r2-Bs-thr_M_signal59.420776
Signal(P)244.093216
Spike_AFFX-r2-Bs-phe_3-5-ratio1.237456
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8378,Count:9
Spike_AFFX-r2-P1-cre_5_signal3413.205811
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8253
Signal(M)16.279875
BackgroundAvg:72.06,Std:0.50,Min:71.0,Max:73.5
Spike_AFFX-r2-Ec-bioC_avg-signal292.584534
Spike_AFFX-r2-Bs-dap_avg-signal133.156860
Spike_AFFX-r2-Bs-dap_3-5-ratio2.860217
Spike_AFFX-r2-Ec-bioB_5_signal72.853851
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.561511
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-10_eyw110_Water_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 ("Keller_585-10_eyw110_Water_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: Keller_585-10_eyw110_Water_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At2g02220
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.635816
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-ratio1.387021
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.985938
Spike_AFFX-r2-Bs-dap_5_signal40.716827
NoiseAvg:3.06,Std:0.08,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_signal26.772110
#P13732
Spike_AFFX-r2-Bs-phe_M_signal33.764614
Corner-Avg:9505,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal101.493462
Spike_AFFX-r2-Ec-bioB_3_signal62.722366
Spike_AFFX-r2-Bs-lys_M_signal6.494857
Spike_AFFX-r2-P1-cre_3_signal4222.081543
Spike_AFFX-r2-Bs-lys_3-5-ratio1.392433
Spike_AFFX-r2-Bs-dap_M_signal145.834518
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.089820
Spike_AFFX-r2-Ec-bioB_avg-signal75.944244
Spike_AFFX-r2-Bs-thr_avg-signal64.642189
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal961.311768
Spike_AFFX-r2-Bs-phe_5_signal28.382832
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1206.405518
RawQ2.942594
Spike_AFFX-r2-Bs-lys_5_signal17.013350
Signal(A)5.141242
%A37.746601
Signal(All)155.360886
Corner+Avg:154,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal310.641663
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.258932
Spike_AFFX-r2-Ec-bioD_avg-signal1083.858643
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.201668
Spike_AFFX-r2-Bs-lys_avg-signal15.732718
Spike_AFFX-r2-P1-cre_avg-signal3633.037109
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.051732
Spike_AFFX-r2-Bs-thr_3_signal109.493111
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-signal30.468790
Spike_AFFX-r2-Bs-dap_3_signal156.582016
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.254958
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal326.974731
#M468
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.689947
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.950048
Spike_AFFX-r2-Bs-thr_M_signal57.661343
Signal(P)254.224625
Spike_AFFX-r2-Bs-phe_3-5-ratio1.030867
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7200,Count:9
Spike_AFFX-r2-P1-cre_5_signal3043.992676
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8610
Signal(M)18.169575
BackgroundAvg:69.81,Std:0.24,Min:69.1,Max:70.9
Spike_AFFX-r2-Ec-bioC_avg-signal318.808197
Spike_AFFX-r2-Bs-dap_avg-signal114.377785
Spike_AFFX-r2-Bs-dap_3-5-ratio3.845634
Spike_AFFX-r2-Ec-bioB_5_signal63.616920
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.635816
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-11_eyw110_Ha_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 ("Keller_585-11_eyw110_Ha_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: Keller_585-11_eyw110_Ha_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At2g02220
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.691806
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-ratio1.012737
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.388252
Spike_AFFX-r2-Bs-dap_5_signal56.088417
NoiseAvg:2.94,Std:0.08,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.031960
#P13924
Spike_AFFX-r2-Bs-phe_M_signal27.619293
Corner-Avg:9470,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal94.358528
Spike_AFFX-r2-Ec-bioB_3_signal79.954269
Spike_AFFX-r2-Bs-lys_M_signal12.688534
Spike_AFFX-r2-P1-cre_3_signal3628.205566
Spike_AFFX-r2-Bs-lys_3-5-ratio1.855775
Spike_AFFX-r2-Bs-dap_M_signal140.613861
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.944094
Spike_AFFX-r2-Ec-bioB_avg-signal77.302101
Spike_AFFX-r2-Bs-thr_avg-signal69.726997
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal876.183289
Spike_AFFX-r2-Bs-phe_5_signal30.461933
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1338.119873
RawQ2.840146
Spike_AFFX-r2-Bs-lys_5_signal22.335661
Signal(A)5.088394
%A36.979397
Signal(All)154.419388
Corner+Avg:143,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal278.115784
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.158289
Spike_AFFX-r2-Ec-bioD_avg-signal1107.151611
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.043404
Spike_AFFX-r2-Bs-lys_avg-signal25.491385
Spike_AFFX-r2-P1-cre_avg-signal3605.389160
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.977203
Spike_AFFX-r2-Bs-thr_3_signal114.504784
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-signal29.746506
Spike_AFFX-r2-Bs-dap_3_signal170.516037
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.527215
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal340.491669
#M451
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.449959
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.816806
Spike_AFFX-r2-Bs-thr_M_signal65.644257
Signal(P)249.284836
Spike_AFFX-r2-Bs-phe_3-5-ratio1.022860
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7605,Count:9
Spike_AFFX-r2-P1-cre_5_signal3582.572998
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8435
Signal(M)18.500124
BackgroundAvg:65.94,Std:0.33,Min:65.2,Max:67.3
Spike_AFFX-r2-Ec-bioC_avg-signal309.303711
Spike_AFFX-r2-Bs-dap_avg-signal122.406097
Spike_AFFX-r2-Bs-dap_3-5-ratio3.040129
Spike_AFFX-r2-Ec-bioB_5_signal57.593502
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.691806
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-12_eyw110_Ha_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 ("Keller_585-12_eyw110_Ha_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: Keller_585-12_eyw110_Ha_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At2g02220
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.386081
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-ratio1.216722
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.203470
Spike_AFFX-r2-Bs-dap_5_signal68.897682
NoiseAvg:3.60,Std:0.09,Min:3.2,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal33.569023
#P14604
Spike_AFFX-r2-Bs-phe_M_signal34.292503
Corner-Avg:11401,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal73.549072
Spike_AFFX-r2-Ec-bioB_3_signal72.800316
Spike_AFFX-r2-Bs-lys_M_signal17.941364
Spike_AFFX-r2-P1-cre_3_signal3778.268066
Spike_AFFX-r2-Bs-lys_3-5-ratio1.691329
Spike_AFFX-r2-Bs-dap_M_signal197.592514
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.516048
Spike_AFFX-r2-Ec-bioB_avg-signal68.947128
Spike_AFFX-r2-Bs-thr_avg-signal78.627869
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal778.787598
Spike_AFFX-r2-Bs-phe_5_signal45.626408
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1055.890503
RawQ3.045376
Spike_AFFX-r2-Bs-lys_5_signal25.909933
Signal(A)4.094673
%A34.064007
Signal(All)149.341812
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal284.696869
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal37.808308
Spike_AFFX-r2-Ec-bioD_avg-signal917.339050
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.024551
Spike_AFFX-r2-Bs-lys_avg-signal29.224510
Spike_AFFX-r2-P1-cre_avg-signal3441.775879
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.911442
Spike_AFFX-r2-Bs-thr_3_signal118.030304
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-signal39.242405
Spike_AFFX-r2-Bs-dap_3_signal236.312607
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.355813
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal265.505127
#M436
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.822231
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.072284
Spike_AFFX-r2-Bs-thr_M_signal84.284286
Signal(P)230.621811
Spike_AFFX-r2-Bs-phe_3-5-ratio0.828650
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9355,Count:9
Spike_AFFX-r2-P1-cre_5_signal3105.283936
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7770
Signal(M)15.298508
BackgroundAvg:77.11,Std:0.70,Min:74.2,Max:78.6
Spike_AFFX-r2-Ec-bioC_avg-signal275.101013
Spike_AFFX-r2-Bs-dap_avg-signal167.600937
Spike_AFFX-r2-Bs-dap_3-5-ratio3.429906
Spike_AFFX-r2-Ec-bioB_5_signal60.491993
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.386081
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-13_egy19_Water_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 ("Keller_585-13_egy19_Water_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: Keller_585-13_egy19_Water_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At3g11340
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.759323
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-ratio1.186650
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.122511
Spike_AFFX-r2-Bs-dap_5_signal93.714073
NoiseAvg:2.86,Std:0.10,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_signal43.761494
#P13679
Spike_AFFX-r2-Bs-phe_M_signal56.416645
Corner-Avg:10102,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal125.057472
Spike_AFFX-r2-Ec-bioB_3_signal101.678650
Spike_AFFX-r2-Bs-lys_M_signal15.637951
Spike_AFFX-r2-P1-cre_3_signal5279.706543
Spike_AFFX-r2-Bs-lys_3-5-ratio1.126009
Spike_AFFX-r2-Bs-dap_M_signal269.547302
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.935806
Spike_AFFX-r2-Ec-bioB_avg-signal105.772522
Spike_AFFX-r2-Bs-thr_avg-signal122.259613
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1225.119385
Spike_AFFX-r2-Bs-phe_5_signal46.784058
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1714.280884
RawQ2.708125
Spike_AFFX-r2-Bs-lys_5_signal29.087774
Signal(A)5.275482
%A38.084175
Signal(All)158.070496
Corner+Avg:168,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal413.473999
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal51.866364
Spike_AFFX-r2-Ec-bioD_avg-signal1469.700195
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.969311
Spike_AFFX-r2-Bs-lys_avg-signal25.826277
Spike_AFFX-r2-P1-cre_avg-signal4864.479492
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_signal215.998245
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-signal51.689022
Spike_AFFX-r2-Bs-dap_3_signal306.505066
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.399277
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal447.655853
#M444
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.753105
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.923643
Spike_AFFX-r2-Bs-thr_M_signal107.019104
Signal(P)259.595581
Spike_AFFX-r2-Bs-phe_3-5-ratio1.108633
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7317,Count:9
Spike_AFFX-r2-P1-cre_5_signal4449.251953
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8687
Signal(M)19.711338
BackgroundAvg:66.51,Std:0.44,Min:65.6,Max:67.6
Spike_AFFX-r2-Ec-bioC_avg-signal430.564941
Spike_AFFX-r2-Bs-dap_avg-signal223.255478
Spike_AFFX-r2-Bs-dap_3-5-ratio3.270641
Spike_AFFX-r2-Ec-bioB_5_signal90.581436
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.759323
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-14_egy19_Water_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 ("Keller_585-14_egy19_Water_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: Keller_585-14_egy19_Water_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At3g11340
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.605467
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-ratio1.539951
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.852059
Spike_AFFX-r2-Bs-dap_5_signal30.164881
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_signal28.143194
#P13591
Spike_AFFX-r2-Bs-phe_M_signal19.897547
Corner-Avg:10155,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.096535
Spike_AFFX-r2-Ec-bioB_3_signal65.162849
Spike_AFFX-r2-Bs-lys_M_signal13.161238
Spike_AFFX-r2-P1-cre_3_signal4560.350098
Spike_AFFX-r2-Bs-lys_3-5-ratio2.024612
Spike_AFFX-r2-Bs-dap_M_signal122.067749
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.337038
Spike_AFFX-r2-Ec-bioB_avg-signal76.912109
Spike_AFFX-r2-Bs-thr_avg-signal47.716297
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal870.488831
Spike_AFFX-r2-Bs-phe_5_signal14.850616
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1323.344482
RawQ2.780847
Spike_AFFX-r2-Bs-lys_5_signal7.748455
Signal(A)4.680930
%A38.360367
Signal(All)155.830307
Corner+Avg:171,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal341.829010
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.869303
Spike_AFFX-r2-Ec-bioD_avg-signal1096.916626
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.583515
Spike_AFFX-r2-Bs-lys_avg-signal12.199101
Spike_AFFX-r2-P1-cre_avg-signal3760.854980
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.056116
Spike_AFFX-r2-Bs-thr_3_signal65.771721
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-signal19.872488
Spike_AFFX-r2-Bs-dap_3_signal116.438820
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.520231
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal386.215790
#M469
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.687613
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.885073
Spike_AFFX-r2-Bs-thr_M_signal49.233986
Signal(P)257.885864
Spike_AFFX-r2-Bs-phe_3-5-ratio1.674631
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7280,Count:9
Spike_AFFX-r2-P1-cre_5_signal2961.359863
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8750
Signal(M)18.346090
BackgroundAvg:69.39,Std:0.36,Min:68.4,Max:70.8
Spike_AFFX-r2-Ec-bioC_avg-signal364.022400
Spike_AFFX-r2-Bs-dap_avg-signal89.557152
Spike_AFFX-r2-Bs-dap_3-5-ratio3.860079
Spike_AFFX-r2-Ec-bioB_5_signal76.476944
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.605467
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-15_egy19_Ha_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 ("Keller_585-15_egy19_Ha_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: Keller_585-15_egy19_Ha_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At3g11340
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.662641
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-ratio0.895247
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.860575
Spike_AFFX-r2-Bs-dap_5_signal98.702454
NoiseAvg:2.96,Std:0.11,Min:2.7,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_signal38.985394
#P14364
Spike_AFFX-r2-Bs-phe_M_signal54.990681
Corner-Avg:10396,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.962280
Spike_AFFX-r2-Ec-bioB_3_signal79.408173
Spike_AFFX-r2-Bs-lys_M_signal14.315090
Spike_AFFX-r2-P1-cre_3_signal3595.454834
Spike_AFFX-r2-Bs-lys_3-5-ratio1.294957
Spike_AFFX-r2-Bs-dap_M_signal252.051132
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.241607
Spike_AFFX-r2-Ec-bioB_avg-signal98.881287
Spike_AFFX-r2-Bs-thr_avg-signal105.728432
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal809.278870
Spike_AFFX-r2-Bs-phe_5_signal37.364761
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1392.598389
RawQ2.878790
Spike_AFFX-r2-Bs-lys_5_signal36.082180
Signal(A)4.601515
%A35.107410
Signal(All)152.307175
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal338.108307
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.420444
Spike_AFFX-r2-Ec-bioD_avg-signal1100.938599
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.972382
Spike_AFFX-r2-Bs-lys_avg-signal32.374043
Spike_AFFX-r2-P1-cre_avg-signal3805.808105
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.920210
Spike_AFFX-r2-Bs-thr_3_signal165.360718
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-signal42.925293
Spike_AFFX-r2-Bs-dap_3_signal355.531891
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.720789
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal310.008362
#M438
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.724857
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.090643
Spike_AFFX-r2-Bs-thr_M_signal112.839195
Signal(P)238.772537
Spike_AFFX-r2-Bs-phe_3-5-ratio0.974727
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9238,Count:9
Spike_AFFX-r2-P1-cre_5_signal4016.161621
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8008
Signal(M)17.235498
BackgroundAvg:70.87,Std:0.50,Min:69.7,Max:72.0
Spike_AFFX-r2-Ec-bioC_avg-signal324.058350
Spike_AFFX-r2-Bs-dap_avg-signal235.428482
Spike_AFFX-r2-Bs-dap_3-5-ratio3.602057
Spike_AFFX-r2-Ec-bioB_5_signal92.273422
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.662641
NF1.000000
HZ4
Tau0.015000

Slide: Keller_585-16_egy19_Ha_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 ("Keller_585-16_egy19_Ha_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: Keller_585-16_egy19_Ha_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: EYW
Stock Code:
Genetic Background: Ws-4
Age: 10 days
Growth Conditions:
Stratification3 days at 4°C
ProtocolSeeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.
Soil ConstituentsCulture Support NF U 44-551 (Engrais Passeron, Vallauris, France) with 5 % quartz sand.
Plant Spacingdense
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: unknownµEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA knock out mutation in At3g11340
Tissue: whole plant
in vivo Treatment: Seven-day-old plants were spray-inoculated to saturation with water or with a spore suspension of the Hyaloperonospora isolate Emwa1 at 40,000 spores/ml. Plants were kept in a growth cabinet at 16°C for 3 d with a 12 h photoperiod.
Additional Organism Information:
Sample DescriptionAerial parts, hypocotyls, cotyledons and leaf primordia
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:0.771765
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-ratio1.144837
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.929283
Spike_AFFX-r2-Bs-dap_5_signal68.163498
NoiseAvg:3.06,Std:0.07,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_signal36.412201
#P13547
Spike_AFFX-r2-Bs-phe_M_signal22.829617
Corner-Avg:9318,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal111.172638
Spike_AFFX-r2-Ec-bioB_3_signal85.349602
Spike_AFFX-r2-Bs-lys_M_signal15.506255
Spike_AFFX-r2-P1-cre_3_signal4403.027832
Spike_AFFX-r2-Bs-lys_3-5-ratio1.597388
Spike_AFFX-r2-Bs-dap_M_signal157.268311
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.380004
Spike_AFFX-r2-Ec-bioB_avg-signal96.122284
Spike_AFFX-r2-Bs-thr_avg-signal65.367088
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal870.430725
Spike_AFFX-r2-Bs-phe_5_signal28.573093
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1478.120850
RawQ2.968997
Spike_AFFX-r2-Bs-lys_5_signal23.920555
Signal(A)5.917517
%A38.443665
Signal(All)154.903366
Corner+Avg:152,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal367.413788
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.379324
Spike_AFFX-r2-Ec-bioD_avg-signal1174.275757
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.390617
Spike_AFFX-r2-Bs-lys_avg-signal25.879068
Spike_AFFX-r2-P1-cre_avg-signal4124.507813
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.165717
Spike_AFFX-r2-Bs-thr_3_signal86.661201
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.594009
Spike_AFFX-r2-Bs-dap_3_signal223.396957
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.698149
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal362.427002
#M494
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.210400
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.013759
Spike_AFFX-r2-Bs-thr_M_signal73.027863
Signal(P)256.195221
Spike_AFFX-r2-Bs-phe_3-5-ratio1.098212
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8860,Count:9
Spike_AFFX-r2-P1-cre_5_signal3845.987793
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8769
Signal(M)21.818825
BackgroundAvg:72.06,Std:0.39,Min:71.2,Max:73.1
Spike_AFFX-r2-Ec-bioC_avg-signal364.920410
Spike_AFFX-r2-Bs-dap_avg-signal149.609604
Spike_AFFX-r2-Bs-dap_3-5-ratio3.277369
Spike_AFFX-r2-Ec-bioB_5_signal91.844612
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.771765
NF1.000000
HZ4
Tau0.015000


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