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Experiment: Comparative gene expression analysis between Arabidopsis wt and wrky33 mutant plants upon Botrytis cinerea infection

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-577

Wrky33 mutant plants are highly susceptible to the fungus Botrytis cinerea (Bc) while wt is not. To identify differentially expressed genes 5 weeks old wt and wrky33 (GABI_324B11) plants were mock treated and spray infected with Bc (isolate 2100 Spanish Type Culture Collection) at 5x105 spores/ml, and kept for 14 hours at high humidity and constant light. To resuspend the spores and for mock treatment Vogel buffer was used (in 1l: 15g sucrose, 3g Na-citrate, 5g K2HPO4, 0.2g MgSO4 7H2O, 0.1g CaCl2 2H2O, 2 g NH4NO3). 100 mg of leaf tissue was collected and total RNA isolated using TRI reagent following the suppliers instructions (Ambion). Leaves from three plants were pooled to make one biological replicate, and samples from three independent biological replicates for each genotype and treatment were submitted to hybridisation against a total number of 12 Arabidopsis ATH1 GeneChip arrays (Affymetrix).

About the Experimenter

Name:Dr Rainer Birkenbihl
Head of Lab Name:Dr Imre Somssich
Lab:
Address:Max-Planck-Institute for Plant Breeding
Dept. Plant-Microbe Interactions
Carl-von-Linné Weg 10
Cologne
Postcode: 50829
Country: Germany
 

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, pathogenicity_design
Number of Slides:12
 
Experimental Parameters:
parameterinfect
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Birkenbihl: Comparative gene expression analysis between Arabidopsis wt and wrky33 mutant plants upon Botrytis cinerea infection_genome

Slide: Birkenbihl_wt_contr_repl_1

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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 ("Birkenbihl_wt_contr_repl_1") 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: Birkenbihl_wt_contr_repl_1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Tissue: rosette leaves
in vivo Treatment: mock treatment with Vogelbuffer
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.805578
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-ratio1.324139
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.168193
Spike_AFFX-r2-Bs-dap_5_signal282.219025
NoiseAvg:2.46,Std:0.07,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal99.602493
#P13324
Spike_AFFX-r2-Bs-phe_M_signal175.728058
Corner-Avg:16058,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal171.781815
Spike_AFFX-r2-Ec-bioB_3_signal148.369049
Spike_AFFX-r2-Bs-lys_M_signal71.048828
Spike_AFFX-r2-P1-cre_3_signal6365.237305
Spike_AFFX-r2-Bs-lys_3-5-ratio1.428300
Spike_AFFX-r2-Bs-dap_M_signal608.770142
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.482875
Spike_AFFX-r2-Ec-bioB_avg-signal149.052719
Spike_AFFX-r2-Bs-thr_avg-signal214.781677
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1497.071777
Spike_AFFX-r2-Bs-phe_5_signal182.619675
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1905.605835
RawQ2.462778
Spike_AFFX-r2-Bs-lys_5_signal82.453476
Signal(A)6.300785
%A39.500217
Signal(All)156.301346
Corner+Avg:91,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal461.839447
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal260.115417
Spike_AFFX-r2-Ec-bioD_avg-signal1701.338867
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.412975
Spike_AFFX-r2-Bs-lys_avg-signal90.423523
Spike_AFFX-r2-P1-cre_avg-signal5586.157715
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.086804
Spike_AFFX-r2-Bs-thr_3_signal346.903046
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-signal206.154373
Spike_AFFX-r2-Bs-dap_3_signal1051.494019
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.272889
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal486.552765
#M476
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal117.768288
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.949207
Spike_AFFX-r2-Bs-thr_M_signal197.839539
Signal(P)262.526733
Spike_AFFX-r2-Bs-phe_3-5-ratio1.424356
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14735,Count:9
Spike_AFFX-r2-P1-cre_5_signal4807.078125
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9010
Signal(M)22.179155
BackgroundAvg:71.70,Std:0.32,Min:70.4,Max:72.5
Spike_AFFX-r2-Ec-bioC_avg-signal474.196106
Spike_AFFX-r2-Bs-dap_avg-signal647.494385
Spike_AFFX-r2-Bs-dap_3-5-ratio3.725808
Spike_AFFX-r2-Ec-bioB_5_signal127.007286
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.805578
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wt_contr_repl_2

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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 ("Birkenbihl_wt_contr_repl_2") 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: Birkenbihl_wt_contr_repl_2
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Tissue: rosette leaves
in vivo Treatment: Mock-treatment with Vogelbuffer.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.885502
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-ratio1.418920
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.982042
Spike_AFFX-r2-Bs-dap_5_signal199.356247
NoiseAvg:2.19,Std:0.09,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal61.695732
#P13395
Spike_AFFX-r2-Bs-phe_M_signal125.232887
Corner-Avg:13546,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal143.700867
Spike_AFFX-r2-Ec-bioB_3_signal127.326660
Spike_AFFX-r2-Bs-lys_M_signal47.757484
Spike_AFFX-r2-P1-cre_3_signal5879.477051
Spike_AFFX-r2-Bs-lys_3-5-ratio1.834277
Spike_AFFX-r2-Bs-dap_M_signal405.998596
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.356023
Spike_AFFX-r2-Ec-bioB_avg-signal133.560852
Spike_AFFX-r2-Bs-thr_avg-signal154.347214
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1160.086426
Spike_AFFX-r2-Bs-phe_5_signal101.277306
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1570.742065
RawQ2.088959
Spike_AFFX-r2-Bs-lys_5_signal61.996258
Signal(A)6.331823
%A39.158264
Signal(All)150.867050
Corner+Avg:78,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal452.302216
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal216.455780
Spike_AFFX-r2-Ec-bioD_avg-signal1365.414307
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.724243
Spike_AFFX-r2-Bs-lys_avg-signal74.490685
Spike_AFFX-r2-P1-cre_avg-signal5011.552734
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.117492
Spike_AFFX-r2-Bs-thr_3_signal268.748016
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-signal147.655319
Spike_AFFX-r2-Bs-dap_3_signal742.104065
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.353987
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal422.100922
#M483
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal113.718300
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.071550
Spike_AFFX-r2-Bs-thr_M_signal132.597885
Signal(P)251.911087
Spike_AFFX-r2-Bs-phe_3-5-ratio2.137259
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11215,Count:9
Spike_AFFX-r2-P1-cre_5_signal4143.628418
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8932
Signal(M)21.475388
BackgroundAvg:65.66,Std:0.88,Min:64.2,Max:68.6
Spike_AFFX-r2-Ec-bioC_avg-signal437.201569
Spike_AFFX-r2-Bs-dap_avg-signal449.152954
Spike_AFFX-r2-Bs-dap_3-5-ratio3.722502
Spike_AFFX-r2-Ec-bioB_5_signal129.655014
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.885502
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wt_contr_repl_3

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 ("Birkenbihl_wt_contr_repl_3") 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: Birkenbihl_wt_contr_repl_3
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Tissue: rosette leaves
in vivo Treatment: Mock-treatment with Vogelbuffer.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:1.053887
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-ratio1.392040
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.882663
Spike_AFFX-r2-Bs-dap_5_signal185.738312
NoiseAvg:2.10,Std:0.05,Min:1.9,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal70.780319
#P12979
Spike_AFFX-r2-Bs-phe_M_signal111.569588
Corner-Avg:13208,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal163.144791
Spike_AFFX-r2-Ec-bioB_3_signal118.172546
Spike_AFFX-r2-Bs-lys_M_signal42.219948
Spike_AFFX-r2-P1-cre_3_signal7445.742188
Spike_AFFX-r2-Bs-lys_3-5-ratio1.738833
Spike_AFFX-r2-Bs-dap_M_signal414.013824
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.260305
Spike_AFFX-r2-Ec-bioB_avg-signal138.399704
Spike_AFFX-r2-Bs-thr_avg-signal172.918518
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1210.813843
Spike_AFFX-r2-Bs-phe_5_signal84.543060
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1717.875366
RawQ2.140229
Spike_AFFX-r2-Bs-lys_5_signal58.295334
Signal(A)7.684445
%A40.977642
Signal(All)159.241348
Corner+Avg:84,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal551.861694
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal170.853134
Spike_AFFX-r2-Ec-bioD_avg-signal1464.344604
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.900482
Spike_AFFX-r2-Bs-lys_avg-signal67.293716
Spike_AFFX-r2-P1-cre_avg-signal6397.270996
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.121876
Spike_AFFX-r2-Bs-thr_3_signal301.545746
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-signal122.321930
Spike_AFFX-r2-Bs-dap_3_signal714.588867
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.418777
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal522.191101
#M484
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal101.365860
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.056819
Spike_AFFX-r2-Bs-thr_M_signal146.429504
Signal(P)273.396484
Spike_AFFX-r2-Bs-phe_3-5-ratio2.020901
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10181,Count:9
Spike_AFFX-r2-P1-cre_5_signal5348.799805
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9347
Signal(M)24.908192
BackgroundAvg:68.25,Std:0.35,Min:67.6,Max:69.4
Spike_AFFX-r2-Ec-bioC_avg-signal537.026367
Spike_AFFX-r2-Bs-dap_avg-signal438.113647
Spike_AFFX-r2-Bs-dap_3-5-ratio3.847288
Spike_AFFX-r2-Ec-bioB_5_signal133.881775
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.053887
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wt_Bc_repl_1

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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 ("Birkenbihl_wt_Bc_repl_1") 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: Birkenbihl_wt_Bc_repl_1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Tissue: rosette leaves
in vivo Treatment: The Botrytis cinerea isolate 2100 (also designated B. cinerea 1.29) from the Spanish Type Culture Collection was cultivated on potato dextrose plates at 22°C for 10 days. Spores were isolated, washed and frozen at -80 °C in 0.8 % NaCl at a concentration of 107 spores/ml. The Arabidopsis plants were spray infected with spores diluted in Vogelbuffer (in 1l: 15g sucrose, 3g Na-citrate, 5g K2HPO4, 0.2g MgSO4 7H2O, 0.1g CaCl2 2H2O, 2 g NH4NO3) to 5x105 spores/ml. For mock-treatment Vogelbuffer alone was used. One day before and during the entire infection process plants were incubated at high humidity and constant light under a hood.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:1.015489
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-ratio1.395259
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.975347
Spike_AFFX-r2-Bs-dap_5_signal163.418503
NoiseAvg:2.33,Std:0.09,Min:2.2,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal63.243877
#P13150
Spike_AFFX-r2-Bs-phe_M_signal103.841469
Corner-Avg:10737,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal169.859650
Spike_AFFX-r2-Ec-bioB_3_signal128.814865
Spike_AFFX-r2-Bs-lys_M_signal41.816727
Spike_AFFX-r2-P1-cre_3_signal6171.202148
Spike_AFFX-r2-Bs-lys_3-5-ratio1.633340
Spike_AFFX-r2-Bs-dap_M_signal325.906616
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.848915
Spike_AFFX-r2-Ec-bioB_avg-signal143.581787
Spike_AFFX-r2-Bs-thr_avg-signal172.118179
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1111.878662
Spike_AFFX-r2-Bs-phe_5_signal81.425964
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1596.340942
RawQ2.324941
Spike_AFFX-r2-Bs-lys_5_signal46.060066
Signal(A)7.613269
%A40.184132
Signal(All)149.312164
Corner+Avg:68,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal596.557617
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal159.251083
Spike_AFFX-r2-Ec-bioD_avg-signal1354.109863
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.650154
Spike_AFFX-r2-Bs-lys_avg-signal54.369507
Spike_AFFX-r2-P1-cre_avg-signal5297.091309
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_signal306.664154
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-signal114.839508
Spike_AFFX-r2-Bs-dap_3_signal628.030457
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.435715
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal510.717041
#M494
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal75.231728
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.168079
Spike_AFFX-r2-Bs-thr_M_signal146.446518
Signal(P)252.781723
Spike_AFFX-r2-Bs-phe_3-5-ratio1.955778
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8605,Count:9
Spike_AFFX-r2-P1-cre_5_signal4422.980469
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9166
Signal(M)24.185383
BackgroundAvg:68.53,Std:0.93,Min:66.9,Max:73.6
Spike_AFFX-r2-Ec-bioC_avg-signal553.637329
Spike_AFFX-r2-Bs-dap_avg-signal372.451874
Spike_AFFX-r2-Bs-dap_3-5-ratio3.843081
Spike_AFFX-r2-Ec-bioB_5_signal132.070862
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.015489
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wt_Bc_repl_2

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 ("Birkenbihl_wt_Bc_repl_2") 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: Birkenbihl_wt_Bc_repl_2
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Tissue: rosette leaves
in vivo Treatment: The Botrytis cinerea isolate 2100 (also designated B. cinerea 1.29) from the Spanish Type Culture Collection was cultivated on potato dextrose plates at 22°C for 10 days. Spores were isolated, washed and frozen at -80 °C in 0.8 % NaCl at a concentration of 107 spores/ml. The Arabidopsis plants were spray infected with spores diluted in Vogelbuffer (in 1l: 15g sucrose, 3g Na-citrate, 5g K2HPO4, 0.2g MgSO4 7H2O, 0.1g CaCl2 2H2O, 2 g NH4NO3) to 5x105 spores/ml. For mock-treatment Vogelbuffer alone was used. One day before and during the entire infection process plants were incubated at high humidity and constant light under a hood.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.61142
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-ratio1.418982
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.816821
Spike_AFFX-r2-Bs-dap_5_signal105.325500
NoiseAvg:2.62,Std:0.07,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.368652
#P14080
Spike_AFFX-r2-Bs-phe_M_signal87.327164
Corner-Avg:12342,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.703400
Spike_AFFX-r2-Ec-bioB_3_signal103.781937
Spike_AFFX-r2-Bs-lys_M_signal58.404503
Spike_AFFX-r2-P1-cre_3_signal5020.846680
Spike_AFFX-r2-Bs-lys_3-5-ratio2.201745
Spike_AFFX-r2-Bs-dap_M_signal337.805908
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.667381
Spike_AFFX-r2-Ec-bioB_avg-signal118.513763
Spike_AFFX-r2-Bs-thr_avg-signal150.644241
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal966.789856
Spike_AFFX-r2-Bs-phe_5_signal70.838791
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1312.679321
RawQ2.558207
Spike_AFFX-r2-Bs-lys_5_signal46.767887
Signal(A)4.616982
%A36.396317
Signal(All)143.841415
Corner+Avg:77,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal413.012085
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal207.149567
Spike_AFFX-r2-Ec-bioD_avg-signal1139.734619
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.727314
Spike_AFFX-r2-Bs-lys_avg-signal69.381119
Spike_AFFX-r2-P1-cre_avg-signal4279.595703
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.876370
Spike_AFFX-r2-Bs-thr_3_signal319.388275
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-signal121.771851
Spike_AFFX-r2-Bs-dap_3_signal741.418823
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.357771
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal375.702087
#M428
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal102.970970
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.099307
Spike_AFFX-r2-Bs-thr_M_signal109.175797
Signal(P)229.792877
Spike_AFFX-r2-Bs-phe_3-5-ratio2.924239
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10673,Count:9
Spike_AFFX-r2-P1-cre_5_signal3538.344971
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8302
Signal(M)16.843119
BackgroundAvg:75.80,Std:0.73,Min:74.3,Max:78.1
Spike_AFFX-r2-Ec-bioC_avg-signal394.357086
Spike_AFFX-r2-Bs-dap_avg-signal394.850098
Spike_AFFX-r2-Bs-dap_3-5-ratio7.039310
Spike_AFFX-r2-Ec-bioB_5_signal127.055962
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.611420
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wt_Bc_repl_3

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 ("Birkenbihl_wt_Bc_repl_3") 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: Birkenbihl_wt_Bc_repl_3
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Tissue: rosette leaves
in vivo Treatment: The Botrytis cinerea isolate 2100 (also designated B. cinerea 1.29) from the Spanish Type Culture Collection was cultivated on potato dextrose plates at 22°C for 10 days. Spores were isolated, washed and frozen at -80 °C in 0.8 % NaCl at a concentration of 107 spores/ml. The Arabidopsis plants were spray infected with spores diluted in Vogelbuffer (in 1l: 15g sucrose, 3g Na-citrate, 5g K2HPO4, 0.2g MgSO4 7H2O, 0.1g CaCl2 2H2O, 2 g NH4NO3) to 5x105 spores/ml. For mock-treatment Vogelbuffer alone was used. One day before and during the entire infection process plants were incubated at high humidity and constant light under a hood.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.613005
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-ratio1.451770
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.155310
Spike_AFFX-r2-Bs-dap_5_signal165.368225
NoiseAvg:2.76,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_signal57.251247
#P13978
Spike_AFFX-r2-Bs-phe_M_signal112.314232
Corner-Avg:13943,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal117.039093
Spike_AFFX-r2-Ec-bioB_3_signal104.237556
Spike_AFFX-r2-Bs-lys_M_signal54.546539
Spike_AFFX-r2-P1-cre_3_signal5086.527832
Spike_AFFX-r2-Bs-lys_3-5-ratio1.627708
Spike_AFFX-r2-Bs-dap_M_signal375.818451
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.829821
Spike_AFFX-r2-Ec-bioB_avg-signal103.833778
Spike_AFFX-r2-Bs-thr_avg-signal158.497894
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal917.285156
Spike_AFFX-r2-Bs-phe_5_signal101.565277
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1298.687134
RawQ2.691497
Spike_AFFX-r2-Bs-lys_5_signal56.962368
Signal(A)5.749259
%A36.742657
Signal(All)145.315689
Corner+Avg:91,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal379.700684
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal180.242477
Spike_AFFX-r2-Ec-bioD_avg-signal1107.986084
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.280140
Spike_AFFX-r2-Bs-lys_avg-signal68.075668
Spike_AFFX-r2-P1-cre_avg-signal4295.100586
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_signal276.513275
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-signal131.373993
Spike_AFFX-r2-Bs-dap_3_signal754.452881
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.415794
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal375.870605
#M451
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal92.718094
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.010190
Spike_AFFX-r2-Bs-thr_M_signal141.729141
Signal(P)233.093597
Spike_AFFX-r2-Bs-phe_3-5-ratio1.774647
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12231,Count:9
Spike_AFFX-r2-P1-cre_5_signal3503.672852
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8381
Signal(M)18.367855
BackgroundAvg:78.84,Std:0.56,Min:76.8,Max:79.9
Spike_AFFX-r2-Ec-bioC_avg-signal377.785645
Spike_AFFX-r2-Bs-dap_avg-signal431.879883
Spike_AFFX-r2-Bs-dap_3-5-ratio4.562260
Spike_AFFX-r2-Ec-bioB_5_signal90.224716
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.613005
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wrky33_contr_repl_1

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 ("Birkenbihl_wrky33_contr_repl_1") 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: Birkenbihl_wrky33_contr_repl_1
Organism: Arabidopsis thaliana
Alias: GK-324B11.01
Stock Code: N306452
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Genetic Variation: T-DNA Insertion
Tissue: rosette leaves
in vivo Treatment: mock treatment with Vogelbuffer
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.764061
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-ratio1.455426
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.972244
Spike_AFFX-r2-Bs-dap_5_signal199.957855
NoiseAvg:2.58,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal66.481163
#P12980
Spike_AFFX-r2-Bs-phe_M_signal138.515396
Corner-Avg:12822,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.809738
Spike_AFFX-r2-Ec-bioB_3_signal100.787445
Spike_AFFX-r2-Bs-lys_M_signal46.859478
Spike_AFFX-r2-P1-cre_3_signal5629.448242
Spike_AFFX-r2-Bs-lys_3-5-ratio2.249600
Spike_AFFX-r2-Bs-dap_M_signal469.465820
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.860694
Spike_AFFX-r2-Ec-bioB_avg-signal109.753975
Spike_AFFX-r2-Bs-thr_avg-signal179.185745
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal980.192017
Spike_AFFX-r2-Bs-phe_5_signal99.939186
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1381.548950
RawQ2.426023
Spike_AFFX-r2-Bs-lys_5_signal65.014717
Signal(A)6.829328
%A40.806664
Signal(All)154.645554
Corner+Avg:79,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal392.192657
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal234.468185
Spike_AFFX-r2-Ec-bioD_avg-signal1180.870483
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.904865
Spike_AFFX-r2-Bs-lys_avg-signal86.043762
Spike_AFFX-r2-P1-cre_avg-signal4748.676758
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.288470
Spike_AFFX-r2-Bs-thr_3_signal323.144592
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-signal157.640915
Spike_AFFX-r2-Bs-dap_3_signal804.775940
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.409468
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal408.455597
#M522
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal146.257080
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.960184
Spike_AFFX-r2-Bs-thr_M_signal147.931534
Signal(P)265.989258
Spike_AFFX-r2-Bs-phe_3-5-ratio2.346109
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11356,Count:9
Spike_AFFX-r2-P1-cre_5_signal3867.905273
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9308
Signal(M)21.756491
BackgroundAvg:77.32,Std:0.51,Min:76.1,Max:78.7
Spike_AFFX-r2-Ec-bioC_avg-signal400.324127
Spike_AFFX-r2-Bs-dap_avg-signal491.399872
Spike_AFFX-r2-Bs-dap_3-5-ratio4.024728
Spike_AFFX-r2-Ec-bioB_5_signal103.664742
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.764061
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wrky33_contr_repl_2

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 ("Birkenbihl_wrky33_contr_repl_2") 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: Birkenbihl_wrky33_contr_repl_2
Organism: Arabidopsis thaliana
Alias: GK-324B11.01
Stock Code: N306452
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Genetic Variation: T-DNA Insertion
Tissue: rosette leaves
in vivo Treatment: mock treatment with Vogelbuffer
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.660867
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-ratio1.425248
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.098933
Spike_AFFX-r2-Bs-dap_5_signal187.069580
NoiseAvg:2.52,Std:0.09,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal52.136745
#P13240
Spike_AFFX-r2-Bs-phe_M_signal140.820419
Corner-Avg:13355,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal139.609787
Spike_AFFX-r2-Ec-bioB_3_signal128.542480
Spike_AFFX-r2-Bs-lys_M_signal61.071529
Spike_AFFX-r2-P1-cre_3_signal5975.927246
Spike_AFFX-r2-Bs-lys_3-5-ratio1.782648
Spike_AFFX-r2-Bs-dap_M_signal481.143463
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.695809
Spike_AFFX-r2-Ec-bioB_avg-signal128.374176
Spike_AFFX-r2-Bs-thr_avg-signal183.513748
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1156.054565
Spike_AFFX-r2-Bs-phe_5_signal132.017014
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1531.899048
RawQ2.443620
Spike_AFFX-r2-Bs-lys_5_signal68.416916
Signal(A)6.196245
%A39.688732
Signal(All)154.851074
Corner+Avg:89,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal427.506805
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal231.490021
Spike_AFFX-r2-Ec-bioD_avg-signal1343.976807
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.044716
Spike_AFFX-r2-Bs-lys_avg-signal83.817253
Spike_AFFX-r2-P1-cre_avg-signal5084.415039
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.266550
Spike_AFFX-r2-Bs-thr_3_signal349.097717
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-signal168.109146
Spike_AFFX-r2-Bs-dap_3_signal879.359802
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.325110
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal465.900330
#M517
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal121.963303
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.917593
Spike_AFFX-r2-Bs-thr_M_signal149.306808
Signal(P)261.739227
Spike_AFFX-r2-Bs-phe_3-5-ratio1.753486
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10252,Count:9
Spike_AFFX-r2-P1-cre_5_signal4192.902344
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9053
Signal(M)20.562893
BackgroundAvg:71.64,Std:0.58,Min:69.7,Max:72.8
Spike_AFFX-r2-Ec-bioC_avg-signal446.703552
Spike_AFFX-r2-Bs-dap_avg-signal515.857605
Spike_AFFX-r2-Bs-dap_3-5-ratio4.700710
Spike_AFFX-r2-Ec-bioB_5_signal116.970238
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.660867
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wrky33_contr_repl_3

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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 ("Birkenbihl_wrky33_contr_repl_3") 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: Birkenbihl_wrky33_contr_repl_3
Organism: Arabidopsis thaliana
Alias: GK-324B11.01
Stock Code: N306452
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Genetic Variation: T-DNA Insertion
Tissue: rosette leaves
in vivo Treatment: mock treatment with Vogelbuffer
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.909956
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-ratio1.414189
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.994976
Spike_AFFX-r2-Bs-dap_5_signal173.883118
NoiseAvg:2.41,Std:0.08,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal50.015839
#P12727
Spike_AFFX-r2-Bs-phe_M_signal123.710907
Corner-Avg:11309,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal127.563156
Spike_AFFX-r2-Ec-bioB_3_signal100.000206
Spike_AFFX-r2-Bs-lys_M_signal46.423550
Spike_AFFX-r2-P1-cre_3_signal5676.235840
Spike_AFFX-r2-Bs-lys_3-5-ratio2.434873
Spike_AFFX-r2-Bs-dap_M_signal419.467194
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.856525
Spike_AFFX-r2-Ec-bioB_avg-signal109.356178
Spike_AFFX-r2-Bs-thr_avg-signal161.874008
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal908.339417
Spike_AFFX-r2-Bs-phe_5_signal87.455254
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1220.314941
RawQ2.459248
Spike_AFFX-r2-Bs-lys_5_signal49.156643
Signal(A)7.769192
%A41.665936
Signal(All)155.784286
Corner+Avg:71,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal415.563843
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal205.293365
Spike_AFFX-r2-Ec-bioD_avg-signal1064.327148
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P55.795704
Spike_AFFX-r2-Bs-lys_avg-signal71.756790
Spike_AFFX-r2-P1-cre_avg-signal4845.005859
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.538360
Spike_AFFX-r2-Bs-thr_3_signal292.919037
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-signal138.819839
Spike_AFFX-r2-Bs-dap_3_signal787.115356
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.343457
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal381.437134
#M579
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal119.690170
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.089469
Spike_AFFX-r2-Bs-thr_M_signal142.687134
Signal(P)272.302124
Spike_AFFX-r2-Bs-phe_3-5-ratio2.347410
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9504,Count:9
Spike_AFFX-r2-P1-cre_5_signal4013.776123
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9504
Signal(M)24.200762
BackgroundAvg:74.96,Std:0.58,Min:73.9,Max:76.8
Spike_AFFX-r2-Ec-bioC_avg-signal398.500488
Spike_AFFX-r2-Bs-dap_avg-signal460.155182
Spike_AFFX-r2-Bs-dap_3-5-ratio4.526692
Spike_AFFX-r2-Ec-bioB_5_signal100.505196
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.909956
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wrky33_Bc_repl_1

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 ("Birkenbihl_wrky33_Bc_repl_1") 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: Birkenbihl_wrky33_Bc_repl_1
Organism: Arabidopsis thaliana
Alias: GK-324B11.01
Stock Code: N306452
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Genetic Variation: T-DNA Insertion
Tissue: rosette leaves
in vivo Treatment: The Botrytis cinerea isolate 2100 (also designated B. cinerea 1.29) from the Spanish Type Culture Collection was cultivated on potato dextrose plates at 22°C for 10 days. Spores were isolated, washed and frozen at -80 °C in 0.8 % NaCl at a concentration of 107 spores/ml. The Arabidopsis plants were spray infected with spores diluted in Vogelbuffer (in 1l: 15g sucrose, 3g Na-citrate, 5g K2HPO4, 0.2g MgSO4 7H2O, 0.1g CaCl2 2H2O, 2 g NH4NO3) to 5x105 spores/ml. For mock-treatment Vogelbuffer alone was used. One day before and during the entire infection process plants were incubated at high humidity and constant light under a hood.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.638974
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-ratio1.428868
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.111296
Spike_AFFX-r2-Bs-dap_5_signal232.929382
NoiseAvg:2.79,Std:0.08,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal58.136444
#P13294
Spike_AFFX-r2-Bs-phe_M_signal140.301117
Corner-Avg:13252,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal125.828293
Spike_AFFX-r2-Ec-bioB_3_signal126.395805
Spike_AFFX-r2-Bs-lys_M_signal64.032768
Spike_AFFX-r2-P1-cre_3_signal5786.061035
Spike_AFFX-r2-Bs-lys_3-5-ratio2.115476
Spike_AFFX-r2-Bs-dap_M_signal493.203278
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.650555
Spike_AFFX-r2-Ec-bioB_avg-signal121.987144
Spike_AFFX-r2-Bs-thr_avg-signal187.317764
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1158.296631
Spike_AFFX-r2-Bs-phe_5_signal140.661194
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1620.366089
RawQ2.675378
Spike_AFFX-r2-Bs-lys_5_signal66.434990
Signal(A)6.642399
%A39.544060
Signal(All)149.156387
Corner+Avg:88,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal452.763275
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal224.069504
Spike_AFFX-r2-Ec-bioD_avg-signal1389.331299
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.281456
Spike_AFFX-r2-Bs-lys_avg-signal90.336464
Spike_AFFX-r2-P1-cre_avg-signal4917.731445
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.174485
Spike_AFFX-r2-Bs-thr_3_signal328.503174
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-signal168.343933
Spike_AFFX-r2-Bs-dap_3_signal1009.597168
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.398921
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal390.732697
#M496
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal140.541626
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.158754
Spike_AFFX-r2-Bs-thr_M_signal175.313690
Signal(P)250.690216
Spike_AFFX-r2-Bs-phe_3-5-ratio1.592973
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11422,Count:9
Spike_AFFX-r2-P1-cre_5_signal4049.402100
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9020
Signal(M)19.490269
BackgroundAvg:80.69,Std:0.51,Min:79.0,Max:81.5
Spike_AFFX-r2-Ec-bioC_avg-signal421.747986
Spike_AFFX-r2-Bs-dap_avg-signal578.576599
Spike_AFFX-r2-Bs-dap_3-5-ratio4.334349
Spike_AFFX-r2-Ec-bioB_5_signal113.737335
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.638974
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wrky33_Bc_repl_2

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 ("Birkenbihl_wrky33_Bc_repl_2") 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: Birkenbihl_wrky33_Bc_repl_2
Organism: Arabidopsis thaliana
Alias: GK-324B11.01
Stock Code: N306452
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Genetic Variation: T-DNA Insertion
Tissue: rosette leaves
in vivo Treatment: The Botrytis cinerea isolate 2100 (also designated B. cinerea 1.29) from the Spanish Type Culture Collection was cultivated on potato dextrose plates at 22°C for 10 days. Spores were isolated, washed and frozen at -80 °C in 0.8 % NaCl at a concentration of 107 spores/ml. The Arabidopsis plants were spray infected with spores diluted in Vogelbuffer (in 1l: 15g sucrose, 3g Na-citrate, 5g K2HPO4, 0.2g MgSO4 7H2O, 0.1g CaCl2 2H2O, 2 g NH4NO3) to 5x105 spores/ml. For mock-treatment Vogelbuffer alone was used. One day before and during the entire infection process plants were incubated at high humidity and constant light under a hood.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.72583
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-ratio1.407768
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.950291
Spike_AFFX-r2-Bs-dap_5_signal192.284912
NoiseAvg:2.67,Std:0.05,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal42.149235
#P12753
Spike_AFFX-r2-Bs-phe_M_signal116.450150
Corner-Avg:11834,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal116.364426
Spike_AFFX-r2-Ec-bioB_3_signal102.222771
Spike_AFFX-r2-Bs-lys_M_signal57.808754
Spike_AFFX-r2-P1-cre_3_signal5320.175781
Spike_AFFX-r2-Bs-lys_3-5-ratio2.513882
Spike_AFFX-r2-Bs-dap_M_signal397.076965
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.231660
Spike_AFFX-r2-Ec-bioB_avg-signal108.719063
Spike_AFFX-r2-Bs-thr_avg-signal164.252213
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal825.411316
Spike_AFFX-r2-Bs-phe_5_signal81.708565
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1216.161621
RawQ2.590542
Spike_AFFX-r2-Bs-lys_5_signal58.169006
Signal(A)6.875106
%A41.749233
Signal(All)149.004120
Corner+Avg:75,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal405.160217
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal232.912689
Spike_AFFX-r2-Ec-bioD_avg-signal1020.786499
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P55.909687
Spike_AFFX-r2-Bs-lys_avg-signal87.402588
Spike_AFFX-r2-P1-cre_avg-signal4549.666992
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.341079
Spike_AFFX-r2-Bs-thr_3_signal304.808929
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-signal143.690475
Spike_AFFX-r2-Bs-dap_3_signal882.767944
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.473401
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal420.002289
#M534
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal146.230011
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.964662
Spike_AFFX-r2-Bs-thr_M_signal145.798508
Signal(P)260.502258
Spike_AFFX-r2-Bs-phe_3-5-ratio2.850530
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10387,Count:9
Spike_AFFX-r2-P1-cre_5_signal3779.157715
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9523
Signal(M)20.837379
BackgroundAvg:78.05,Std:0.59,Min:76.6,Max:79.5
Spike_AFFX-r2-Ec-bioC_avg-signal412.581238
Spike_AFFX-r2-Bs-dap_avg-signal490.709961
Spike_AFFX-r2-Bs-dap_3-5-ratio4.590937
Spike_AFFX-r2-Ec-bioB_5_signal107.570007
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.725830
NF1.000000
HZ4
Tau0.015000

Slide: Birkenbihl_wrky33_Bc_repl_3

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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 ("Birkenbihl_wrky33_Bc_repl_3") 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: Birkenbihl_wrky33_Bc_repl_3
Organism: Arabidopsis thaliana
Alias: GK-324B11.01
Stock Code: N306452
Age: 35 days
Growth Conditions:
StratificationSeeds on soil were kept for 48 h at 4°C.
ProtocolPlants were grown for five week under short day conditions in closed cabinets (Schneijder–chambers) on 42 mm Jiffy-7 pots (Jiffy, Denmark), to prevent pathogen infection from garden soil. Before sewing the Jiffy pots peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany). Plants were watered twice a week from below.
Soil Constituents42 mm peat pellets, Jiffy-7 pots (Jiffy, Denmark). Before sewing the peat pellets were soaked in water containing 0.1 % of liquid fertilizer “Wuxal” (Manna, Germany).
Plant Spacing2 per pot
watertwice a week from below
Temperature21 °C average, 22 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.70
Genetic Variation: T-DNA Insertion
Tissue: rosette leaves
in vivo Treatment: The Botrytis cinerea isolate 2100 (also designated B. cinerea 1.29) from the Spanish Type Culture Collection was cultivated on potato dextrose plates at 22°C for 10 days. Spores were isolated, washed and frozen at -80 °C in 0.8 % NaCl at a concentration of 107 spores/ml. The Arabidopsis plants were spray infected with spores diluted in Vogelbuffer (in 1l: 15g sucrose, 3g Na-citrate, 5g K2HPO4, 0.2g MgSO4 7H2O, 0.1g CaCl2 2H2O, 2 g NH4NO3) to 5x105 spores/ml. For mock-treatment Vogelbuffer alone was used. One day before and during the entire infection process plants were incubated at high humidity and constant light under a hood.
Additional Organism Information:
Sample DescriptionThe plants were 5 weeks old, had many rosette leaves and no buds. Typical short day plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.798585
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-ratio1.437662
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.838035
Spike_AFFX-r2-Bs-dap_5_signal162.915497
NoiseAvg:2.42,Std:0.11,Min:2.2,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal50.343971
#P12849
Spike_AFFX-r2-Bs-phe_M_signal121.253983
Corner-Avg:10498,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal110.001526
Spike_AFFX-r2-Ec-bioB_3_signal91.307083
Spike_AFFX-r2-Bs-lys_M_signal43.909348
Spike_AFFX-r2-P1-cre_3_signal5068.125977
Spike_AFFX-r2-Bs-lys_3-5-ratio2.243417
Spike_AFFX-r2-Bs-dap_M_signal381.898254
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.179482
Spike_AFFX-r2-Ec-bioB_avg-signal103.420784
Spike_AFFX-r2-Bs-thr_avg-signal163.500534
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal947.083801
Spike_AFFX-r2-Bs-phe_5_signal88.689636
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1328.696045
RawQ2.436330
Spike_AFFX-r2-Bs-lys_5_signal51.576042
Signal(A)6.569281
%A41.231915
Signal(All)146.627029
Corner+Avg:70,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal435.675995
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal164.724701
Spike_AFFX-r2-Ec-bioD_avg-signal1137.889893
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.330555
Spike_AFFX-r2-Bs-lys_avg-signal70.397316
Spike_AFFX-r2-P1-cre_avg-signal4296.690918
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.437527
Spike_AFFX-r2-Bs-thr_3_signal311.099640
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-signal124.889442
Spike_AFFX-r2-Bs-dap_3_signal727.450500
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.402934
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal397.178101
#M556
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal115.706551
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.096929
Spike_AFFX-r2-Bs-thr_M_signal129.057983
Signal(P)254.622849
Spike_AFFX-r2-Bs-phe_3-5-ratio1.857316
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8789,Count:9
Spike_AFFX-r2-P1-cre_5_signal3525.255615
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9405
Signal(M)20.017130
BackgroundAvg:72.45,Std:1.10,Min:70.7,Max:76.3
Spike_AFFX-r2-Ec-bioC_avg-signal416.427063
Spike_AFFX-r2-Bs-dap_avg-signal424.088104
Spike_AFFX-r2-Bs-dap_3-5-ratio4.465201
Spike_AFFX-r2-Ec-bioB_5_signal108.953743
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.798585
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team