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Experiment: P G62 study

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-590

Analysis of root transcriptome of wild type (Col-0) and mutant (pen1-3) Arabidopsis plants after seed inoculation with the growth promoting rhizobacterium Pseudomonas sp. G62.

About the Experimenter

Name: Melanie Schwochow
Head of Lab Name:Dr Joost van Dongen
Lab:
Address:Department 1: Molecular Physiology, Max-Planck-Institut fur Molekulare Pflanzenphysiologie
Wissenschaftspark Golm, Am Mühlenberg1, Potsdam, Golm, Brandenburg, 14476, GERMANY
Postcode:
Country:
 
Telephone Number: 0331-5678345

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, stimulus_or_stress_design
Number of Slides:12
 
Experimental Parameters:
parameterrhizobacterium treatment of seeds
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Schwochow: P G62 study

Slide: Schwochow_590-1_Col-0_Control_Root_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Schwochow_590-1_Col-0_Control_Root_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-1_Col-0_Control_Root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4°C in the dark - after sterilisation seeds stored over night in tap water at 4°C in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18°C night: 16°C
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.365703
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-ratio1.053309
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.761540
Spike_AFFX-r2-Bs-dap_5_signal40.485203
NoiseAvg:3.49,Std:0.12,Min:3.3,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.521230
#P15813
Spike_AFFX-r2-Bs-phe_M_signal16.601942
Corner-Avg:10631,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal54.141640
Spike_AFFX-r2-Ec-bioB_3_signal31.601351
Spike_AFFX-r2-Bs-lys_M_signal18.224724
Spike_AFFX-r2-P1-cre_3_signal2171.341309
Spike_AFFX-r2-Bs-lys_3-5-ratio1.978127
Spike_AFFX-r2-Bs-dap_M_signal119.104889
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.536582
Spike_AFFX-r2-Ec-bioB_avg-signal42.413219
Spike_AFFX-r2-Bs-thr_avg-signal64.613556
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal348.541565
Spike_AFFX-r2-Bs-phe_5_signal16.715233
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal572.292725
RawQ2.850823
Spike_AFFX-r2-Bs-lys_5_signal14.215601
Signal(A)3.337435
%A29.127575
Signal(All)133.411331
Corner+Avg:191,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal161.130508
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.916233
Spike_AFFX-r2-Ec-bioD_avg-signal460.417145
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.324860
Spike_AFFX-r2-Bs-lys_avg-signal20.186865
Spike_AFFX-r2-P1-cre_avg-signal2116.394775
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.547567
Spike_AFFX-r2-Bs-thr_3_signal131.930969
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-signal22.411135
Spike_AFFX-r2-Bs-dap_3_signal201.325806
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.641964
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal147.877716
#M353
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.120266
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.089620
Spike_AFFX-r2-Bs-thr_M_signal49.388477
Signal(P)190.769821
Spike_AFFX-r2-Bs-phe_3-5-ratio2.029061
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7556,Count:9
Spike_AFFX-r2-P1-cre_5_signal2061.448242
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6644
Signal(M)12.168418
BackgroundAvg:65.92,Std:0.79,Min:64.2,Max:67.9
Spike_AFFX-r2-Ec-bioC_avg-signal154.504120
Spike_AFFX-r2-Bs-dap_avg-signal120.305298
Spike_AFFX-r2-Bs-dap_3-5-ratio4.972825
Spike_AFFX-r2-Ec-bioB_5_signal41.496666
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.365703
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-2_Col-0_Control_Root_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-2_Col-0_Control_Root_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-2_Col-0_Control_Root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4°C in the dark - after sterilisation seeds stored over night in tap water at 4°C in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18°C night: 16°C
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.351385
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.996086
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.752474
Spike_AFFX-r2-Bs-dap_5_signal26.391695
NoiseAvg:3.29,Std:0.08,Min:3.1,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.936382
#P16079
Spike_AFFX-r2-Bs-phe_M_signal13.218464
Corner-Avg:11405,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal60.834545
Spike_AFFX-r2-Ec-bioB_3_signal39.044140
Spike_AFFX-r2-Bs-lys_M_signal11.398717
Spike_AFFX-r2-P1-cre_3_signal1967.272217
Spike_AFFX-r2-Bs-lys_3-5-ratio2.169655
Spike_AFFX-r2-Bs-dap_M_signal112.472580
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.963431
Spike_AFFX-r2-Ec-bioB_avg-signal50.588806
Spike_AFFX-r2-Bs-thr_avg-signal47.414158
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal378.772797
Spike_AFFX-r2-Bs-phe_5_signal25.157000
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal651.582764
RawQ2.963678
Spike_AFFX-r2-Bs-lys_5_signal11.816626
Signal(A)2.526174
%A28.364752
Signal(All)133.233536
Corner+Avg:191,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.675461
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.289488
Spike_AFFX-r2-Ec-bioD_avg-signal515.177795
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.491013
Spike_AFFX-r2-Bs-lys_avg-signal16.284449
Spike_AFFX-r2-P1-cre_avg-signal1971.137451
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.144235
Spike_AFFX-r2-Bs-thr_3_signal90.081612
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.888315
Spike_AFFX-r2-Bs-dap_3_signal149.591415
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.720247
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal148.776947
#M261
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.638004
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.066533
Spike_AFFX-r2-Bs-thr_M_signal39.224472
Signal(P)187.820145
Spike_AFFX-r2-Bs-phe_3-5-ratio0.846265
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8173,Count:9
Spike_AFFX-r2-P1-cre_5_signal1975.002808
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6470
Signal(M)10.546302
BackgroundAvg:71.56,Std:0.99,Min:69.3,Max:73.7
Spike_AFFX-r2-Ec-bioC_avg-signal153.726196
Spike_AFFX-r2-Bs-dap_avg-signal96.151894
Spike_AFFX-r2-Bs-dap_3-5-ratio5.668125
Spike_AFFX-r2-Ec-bioB_5_signal51.887726
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.351385
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-3_Col-0_Control_Root_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-3_Col-0_Control_Root_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-3_Col-0_Control_Root_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4°C in the dark - after sterilisation seeds stored over night in tap water at 4°C in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18°C night: 16°C
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.350441
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.972930
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.805173
Spike_AFFX-r2-Bs-dap_5_signal39.780968
NoiseAvg:3.26,Std:0.12,Min:3.0,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.288088
#P16138
Spike_AFFX-r2-Bs-phe_M_signal18.017504
Corner-Avg:11171,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal52.347626
Spike_AFFX-r2-Ec-bioB_3_signal39.456871
Spike_AFFX-r2-Bs-lys_M_signal8.703444
Spike_AFFX-r2-P1-cre_3_signal1830.219727
Spike_AFFX-r2-Bs-lys_3-5-ratio2.162861
Spike_AFFX-r2-Bs-dap_M_signal94.410103
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.634248
Spike_AFFX-r2-Ec-bioB_avg-signal46.936230
Spike_AFFX-r2-Bs-thr_avg-signal42.697113
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal292.513245
Spike_AFFX-r2-Bs-phe_5_signal19.976357
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal512.410767
RawQ2.965338
Spike_AFFX-r2-Bs-lys_5_signal8.857590
Signal(A)2.736787
%A27.926348
Signal(All)132.785309
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal163.829315
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.968857
Spike_AFFX-r2-Ec-bioD_avg-signal402.462006
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.749672
Spike_AFFX-r2-Bs-lys_avg-signal12.239589
Spike_AFFX-r2-P1-cre_avg-signal1855.680786
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.323981
Spike_AFFX-r2-Bs-thr_3_signal69.234131
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-signal20.320906
Spike_AFFX-r2-Bs-dap_3_signal170.157806
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.751752
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal152.397537
#M302
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.157732
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.075013
Spike_AFFX-r2-Bs-thr_M_signal46.569122
Signal(P)186.417786
Spike_AFFX-r2-Bs-phe_3-5-ratio1.149802
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8910,Count:9
Spike_AFFX-r2-P1-cre_5_signal1881.141846
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6370
Signal(M)9.898938
BackgroundAvg:70.32,Std:0.95,Min:68.1,Max:73.0
Spike_AFFX-r2-Ec-bioC_avg-signal158.113434
Spike_AFFX-r2-Bs-dap_avg-signal101.449623
Spike_AFFX-r2-Bs-dap_3-5-ratio4.277367
Spike_AFFX-r2-Ec-bioB_5_signal49.004196
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.350441
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-4_Col-0_Bacteria_Root_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Schwochow_590-4_Col-0_Bacteria_Root_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-4_Col-0_Bacteria_Root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4°C in the dark - after sterilisation seeds stored over night in tap water at 4°C in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18°C night: 16°C
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.237447
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-ratio1.160031
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.787977
Spike_AFFX-r2-Bs-dap_5_signal39.896664
NoiseAvg:3.28,Std:0.11,Min:3.0,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.601357
#P16546
Spike_AFFX-r2-Bs-phe_M_signal16.140663
Corner-Avg:11838,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal54.122879
Spike_AFFX-r2-Ec-bioB_3_signal32.006809
Spike_AFFX-r2-Bs-lys_M_signal12.137753
Spike_AFFX-r2-P1-cre_3_signal2236.062256
Spike_AFFX-r2-Bs-lys_3-5-ratio1.534008
Spike_AFFX-r2-Bs-dap_M_signal128.213684
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.425169
Spike_AFFX-r2-Ec-bioB_avg-signal42.249542
Spike_AFFX-r2-Bs-thr_avg-signal41.179279
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal357.880920
Spike_AFFX-r2-Bs-phe_5_signal19.528759
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal481.776550
RawQ2.711129
Spike_AFFX-r2-Bs-lys_5_signal14.146266
Signal(A)1.894808
%A26.286716
Signal(All)130.107773
Corner+Avg:199,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal154.105545
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.525700
Spike_AFFX-r2-Ec-bioD_avg-signal419.828735
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P72.538361
Spike_AFFX-r2-Bs-lys_avg-signal15.994834
Spike_AFFX-r2-P1-cre_avg-signal2081.824951
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.174923
Spike_AFFX-r2-Bs-thr_3_signal64.613464
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.398375
Spike_AFFX-r2-Bs-dap_3_signal190.394226
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.346192
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal149.880219
#M268
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.700481
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.028191
Spike_AFFX-r2-Bs-thr_M_signal44.323009
Signal(P)178.558670
Spike_AFFX-r2-Bs-phe_3-5-ratio0.999843
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9237,Count:9
Spike_AFFX-r2-P1-cre_5_signal1927.587769
Spike_AFFX-r2-Bs-phe_M_detectionP
#A5996
Signal(M)7.333363
BackgroundAvg:64.24,Std:0.87,Min:61.4,Max:66.8
Spike_AFFX-r2-Ec-bioC_avg-signal151.992889
Spike_AFFX-r2-Bs-dap_avg-signal119.501526
Spike_AFFX-r2-Bs-dap_3-5-ratio4.772184
Spike_AFFX-r2-Ec-bioB_5_signal40.618942
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.237447
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-5_Col-0_Bacteria_Root_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-5_Col-0_Bacteria_Root_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-5_Col-0_Bacteria_Root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: - measure OD (around 0,6) - take 2ml „³ centrifuge for 1 minute at 12000rpm - discard supernatant - wash pellet with 10mM MgSO4 „³ centrifuge for 1minute at 12000rpm - discard supernatant - resolve the bacteria pellet in 2ml 10mM MgSO4 - discard tap water from the seeds - bacteria solution to the seeds - incubate for 3 hours - shake slightly every 30 minutes
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.343723
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.868647
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.714437
Spike_AFFX-r2-Bs-dap_5_signal39.102627
NoiseAvg:3.28,Std:0.10,Min:3.0,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.752814
#P16056
Spike_AFFX-r2-Bs-phe_M_signal12.534838
Corner-Avg:11438,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal58.316273
Spike_AFFX-r2-Ec-bioB_3_signal32.492302
Spike_AFFX-r2-Bs-lys_M_signal11.647453
Spike_AFFX-r2-P1-cre_3_signal1742.162476
Spike_AFFX-r2-Bs-lys_3-5-ratio1.424413
Spike_AFFX-r2-Bs-dap_M_signal83.515503
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.493251
Spike_AFFX-r2-Ec-bioB_avg-signal45.429394
Spike_AFFX-r2-Bs-thr_avg-signal41.228661
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal328.240662
Spike_AFFX-r2-Bs-phe_5_signal18.995869
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal534.964783
RawQ2.907825
Spike_AFFX-r2-Bs-lys_5_signal13.866982
Signal(A)2.580179
%A28.237616
Signal(All)132.245560
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal159.128326
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.174784
Spike_AFFX-r2-Ec-bioD_avg-signal431.602722
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.390182
Spike_AFFX-r2-Bs-lys_avg-signal15.088914
Spike_AFFX-r2-P1-cre_avg-signal1873.883789
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.372205
Spike_AFFX-r2-Bs-thr_3_signal63.327477
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-signal16.235163
Spike_AFFX-r2-Bs-dap_3_signal149.100708
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.629794
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal144.973984
#M313
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.752308
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.097634
Spike_AFFX-r2-Bs-thr_M_signal50.605686
Signal(P)186.639130
Spike_AFFX-r2-Bs-phe_3-5-ratio0.904133
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9352,Count:9
Spike_AFFX-r2-P1-cre_5_signal2005.605225
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6441
Signal(M)10.301574
BackgroundAvg:70.34,Std:1.22,Min:67.4,Max:73.3
Spike_AFFX-r2-Ec-bioC_avg-signal152.051147
Spike_AFFX-r2-Bs-dap_avg-signal90.572945
Spike_AFFX-r2-Bs-dap_3-5-ratio3.813061
Spike_AFFX-r2-Ec-bioB_5_signal45.479599
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.343723
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-6_Col-0_Bacteria_Root_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-6_Col-0_Bacteria_Root_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-6_Col-0_Bacteria_Root_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: - measure OD (around 0,6) - take 2ml „³ centrifuge for 1 minute at 12000rpm - discard supernatant - wash pellet with 10mM MgSO4 „³ centrifuge for 1minute at 12000rpm - discard supernatant - resolve the bacteria pellet in 2ml 10mM MgSO4 - discard tap water from the seeds - bacteria solution to the seeds - incubate for 3 hours - shake slightly every 30 minutes
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.444468
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.891685
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.823776
Spike_AFFX-r2-Bs-dap_5_signal41.026356
NoiseAvg:2.83,Std:0.10,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.740242
#P15852
Spike_AFFX-r2-Bs-phe_M_signal15.705074
Corner-Avg:10621,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal63.016399
Spike_AFFX-r2-Ec-bioB_3_signal41.711613
Spike_AFFX-r2-Bs-lys_M_signal13.220565
Spike_AFFX-r2-P1-cre_3_signal1804.658447
Spike_AFFX-r2-Bs-lys_3-5-ratio2.083720
Spike_AFFX-r2-Bs-dap_M_signal109.964340
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.206283
Spike_AFFX-r2-Ec-bioB_avg-signal51.787548
Spike_AFFX-r2-Bs-thr_avg-signal48.026661
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal348.171112
Spike_AFFX-r2-Bs-phe_5_signal18.842215
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal601.762695
RawQ2.713167
Spike_AFFX-r2-Bs-lys_5_signal12.529392
Signal(A)2.776738
%A29.158264
Signal(All)134.021927
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal169.800766
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.220234
Spike_AFFX-r2-Ec-bioD_avg-signal474.966919
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.495834
Spike_AFFX-r2-Bs-lys_avg-signal17.285902
Spike_AFFX-r2-P1-cre_avg-signal1914.266357
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.345901
Spike_AFFX-r2-Bs-thr_3_signal83.033051
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.922508
Spike_AFFX-r2-Bs-dap_3_signal188.159760
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.728353
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal201.450851
#M307
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.107748
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.842889
Spike_AFFX-r2-Bs-thr_M_signal41.306698
Signal(P)191.472427
Spike_AFFX-r2-Bs-phe_3-5-ratio1.179279
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8047,Count:9
Spike_AFFX-r2-P1-cre_5_signal2023.874390
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6651
Signal(M)10.915201
BackgroundAvg:64.81,Std:0.71,Min:63.1,Max:66.7
Spike_AFFX-r2-Ec-bioC_avg-signal185.625809
Spike_AFFX-r2-Bs-dap_avg-signal113.050148
Spike_AFFX-r2-Bs-dap_3-5-ratio4.586314
Spike_AFFX-r2-Ec-bioB_5_signal50.634636
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.444468
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-7_pen1-3_Control_Root_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-7_pen1-3_Control_Root_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-7_pen1-3_Control_Root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pen1-3
Stock Code:
Genetic Background: Col-3
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Genetic Variation: EMS induced mutation mutation in AT1G 11310.1
Tissue: roots
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.273494
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-ratio1.214118
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.584592
Spike_AFFX-r2-Bs-dap_5_signal38.419582
NoiseAvg:3.41,Std:0.06,Min:3.3,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.122776
#P16070
Spike_AFFX-r2-Bs-phe_M_signal12.800045
Corner-Avg:11616,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal51.146564
Spike_AFFX-r2-Ec-bioB_3_signal27.444788
Spike_AFFX-r2-Bs-lys_M_signal10.783260
Spike_AFFX-r2-P1-cre_3_signal2272.726318
Spike_AFFX-r2-Bs-lys_3-5-ratio1.207484
Spike_AFFX-r2-Bs-dap_M_signal113.943520
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.515194
Spike_AFFX-r2-Ec-bioB_avg-signal41.846088
Spike_AFFX-r2-Bs-thr_avg-signal31.506216
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal302.748596
Spike_AFFX-r2-Bs-phe_5_signal17.311562
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal428.948639
RawQ2.787409
Spike_AFFX-r2-Bs-lys_5_signal15.167691
Signal(A)2.462676
%A28.092941
Signal(All)130.911026
Corner+Avg:202,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal135.063812
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.716230
Spike_AFFX-r2-Ec-bioD_avg-signal365.848633
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.451553
Spike_AFFX-r2-Bs-lys_avg-signal14.755230
Spike_AFFX-r2-P1-cre_avg-signal2072.321289
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.455502
Spike_AFFX-r2-Bs-thr_3_signal45.706299
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-signal16.942612
Spike_AFFX-r2-Bs-dap_3_signal136.892700
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.416848
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal135.864441
#M332
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.314739
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.994107
Spike_AFFX-r2-Bs-thr_M_signal38.689568
Signal(P)184.621002
Spike_AFFX-r2-Bs-phe_3-5-ratio1.196670
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9031,Count:9
Spike_AFFX-r2-P1-cre_5_signal1871.916138
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6408
Signal(M)10.362113
BackgroundAvg:68.88,Std:0.80,Min:66.1,Max:71.2
Spike_AFFX-r2-Ec-bioC_avg-signal135.464127
Spike_AFFX-r2-Bs-dap_avg-signal96.418602
Spike_AFFX-r2-Bs-dap_3-5-ratio3.563097
Spike_AFFX-r2-Ec-bioB_5_signal46.946911
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.273494
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-8_pen1-3_Control_Root_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-8_pen1-3_Control_Root_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-8_pen1-3_Control_Root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pen1-3
Stock Code:
Genetic Background: Col-3
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Genetic Variation: EMS induced mutation mutation in AT1G 11310.1
Tissue: roots
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.23634
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-ratio1.039060
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.632721
Spike_AFFX-r2-Bs-dap_5_signal40.026508
NoiseAvg:3.36,Std:0.15,Min:3.0,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.671941
#P16326
Spike_AFFX-r2-Bs-phe_M_signal17.669060
Corner-Avg:12126,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal56.263474
Spike_AFFX-r2-Ec-bioB_3_signal31.082300
Spike_AFFX-r2-Bs-lys_M_signal12.980395
Spike_AFFX-r2-P1-cre_3_signal2045.788696
Spike_AFFX-r2-Bs-lys_3-5-ratio1.807494
Spike_AFFX-r2-Bs-dap_M_signal111.665100
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.346108
Spike_AFFX-r2-Ec-bioB_avg-signal45.490185
Spike_AFFX-r2-Bs-thr_avg-signal45.576466
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal357.135864
Spike_AFFX-r2-Bs-phe_5_signal16.357864
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal523.895508
RawQ2.808598
Spike_AFFX-r2-Bs-lys_5_signal13.684493
Signal(A)2.041732
%A27.176678
Signal(All)130.053604
Corner+Avg:211,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal165.338913
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.239819
Spike_AFFX-r2-Ec-bioD_avg-signal440.515686
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.573868
Spike_AFFX-r2-Bs-lys_avg-signal17.133177
Spike_AFFX-r2-P1-cre_avg-signal2007.335938
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.249452
Spike_AFFX-r2-Bs-thr_3_signal78.437782
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.755581
Spike_AFFX-r2-Bs-dap_3_signal199.584183
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.466936
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal140.994934
#M285
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.734642
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.172659
Spike_AFFX-r2-Bs-thr_M_signal43.619678
Signal(P)180.767410
Spike_AFFX-r2-Bs-phe_3-5-ratio1.359580
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9537,Count:9
Spike_AFFX-r2-P1-cre_5_signal1968.883179
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6199
Signal(M)9.324244
BackgroundAvg:69.67,Std:0.77,Min:67.8,Max:71.8
Spike_AFFX-r2-Ec-bioC_avg-signal153.166931
Spike_AFFX-r2-Bs-dap_avg-signal117.091927
Spike_AFFX-r2-Bs-dap_3-5-ratio4.986300
Spike_AFFX-r2-Ec-bioB_5_signal49.124775
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.236340
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-9_pen1-3_Control_Root_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Schwochow_590-9_pen1-3_Control_Root_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-9_pen1-3_Control_Root_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pen1-3
Stock Code:
Genetic Background: Col-3
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Genetic Variation: EMS induced mutation mutation in AT1G 11310.1
Tissue: roots
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.341454
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.900104
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.668601
Spike_AFFX-r2-Bs-dap_5_signal39.278614
NoiseAvg:3.19,Std:0.08,Min:3.0,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.850418
#P16040
Spike_AFFX-r2-Bs-phe_M_signal15.098686
Corner-Avg:9830,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal55.835079
Spike_AFFX-r2-Ec-bioB_3_signal30.843792
Spike_AFFX-r2-Bs-lys_M_signal10.240811
Spike_AFFX-r2-P1-cre_3_signal1776.316284
Spike_AFFX-r2-Bs-lys_3-5-ratio3.505017
Spike_AFFX-r2-Bs-dap_M_signal109.629257
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.148586
Spike_AFFX-r2-Ec-bioB_avg-signal44.270229
Spike_AFFX-r2-Bs-thr_avg-signal56.297703
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal333.256897
Spike_AFFX-r2-Bs-phe_5_signal17.889582
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal561.013977
RawQ2.664424
Spike_AFFX-r2-Bs-lys_5_signal10.957137
Signal(A)2.732548
%A28.474354
Signal(All)131.642380
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal148.491547
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.339752
Spike_AFFX-r2-Ec-bioD_avg-signal447.135437
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.320038
Spike_AFFX-r2-Bs-lys_avg-signal19.867634
Spike_AFFX-r2-P1-cre_avg-signal1874.886475
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.205612
Spike_AFFX-r2-Bs-thr_3_signal103.606239
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-signal16.442673
Spike_AFFX-r2-Bs-dap_3_signal174.893326
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.683428
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal140.830048
#M275
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.404953
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.054402
Spike_AFFX-r2-Bs-thr_M_signal48.436455
Signal(P)185.923981
Spike_AFFX-r2-Bs-phe_3-5-ratio0.913367
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7249,Count:9
Spike_AFFX-r2-P1-cre_5_signal1973.456543
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6495
Signal(M)10.160377
BackgroundAvg:64.17,Std:0.72,Min:62.0,Max:65.6
Spike_AFFX-r2-Ec-bioC_avg-signal144.660797
Spike_AFFX-r2-Bs-dap_avg-signal107.933739
Spike_AFFX-r2-Bs-dap_3-5-ratio4.452635
Spike_AFFX-r2-Ec-bioB_5_signal46.131817
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.341454
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-10_pen1-3_Bacteria_Root_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-10_pen1-3_Bacteria_Root_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-10_pen1-3_Bacteria_Root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pen1-3
Stock Code:
Genetic Background: Col-3
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Genetic Variation: EMS induced mutation mutation in AT1G 11310.1
Tissue: roots
in vivo Treatment: - measure OD (around 0,6) - take 2ml „³ centrifuge for 1 minute at 12000rpm - discard supernatant - wash pellet with 10mM MgSO4 „³ centrifuge for 1minute at 12000rpm - discard supernatant - resolve the bacteria pellet in 2ml 10mM MgSO4 - discard tap water from the seeds - bacteria solution to the seeds - incubate for 3 hours - shake slightly every 30 minutes
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.289382
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-ratio1.053061
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.660195
Spike_AFFX-r2-Bs-dap_5_signal22.775387
NoiseAvg:3.39,Std:0.26,Min:2.8,Max:4.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.344305
#P16343
Spike_AFFX-r2-Bs-phe_M_signal10.175281
Corner-Avg:10985,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal58.731586
Spike_AFFX-r2-Ec-bioB_3_signal35.467937
Spike_AFFX-r2-Bs-lys_M_signal7.072969
Spike_AFFX-r2-P1-cre_3_signal2006.474976
Spike_AFFX-r2-Bs-lys_3-5-ratio1.538771
Spike_AFFX-r2-Bs-dap_M_signal91.066353
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.246659
Spike_AFFX-r2-Ec-bioB_avg-signal49.307644
Spike_AFFX-r2-Bs-thr_avg-signal43.776672
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal350.239471
Spike_AFFX-r2-Bs-phe_5_signal16.930956
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal574.931641
RawQ2.816113
Spike_AFFX-r2-Bs-lys_5_signal13.122919
Signal(A)2.248459
%A27.194214
Signal(All)130.992035
Corner+Avg:186,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal149.000290
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.656370
Spike_AFFX-r2-Ec-bioD_avg-signal462.585571
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.648399
Spike_AFFX-r2-Bs-lys_avg-signal13.463019
Spike_AFFX-r2-P1-cre_avg-signal1955.924072
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.157387
Spike_AFFX-r2-Bs-thr_3_signal82.598892
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-signal15.587535
Spike_AFFX-r2-Bs-dap_3_signal144.780716
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.641539
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal165.471237
#M264
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.193169
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.900460
Spike_AFFX-r2-Bs-thr_M_signal41.386818
Signal(P)181.824554
Spike_AFFX-r2-Bs-phe_3-5-ratio1.160972
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8125,Count:9
Spike_AFFX-r2-P1-cre_5_signal1905.373047
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6203
Signal(M)9.175190
BackgroundAvg:69.74,Std:0.73,Min:68.1,Max:71.8
Spike_AFFX-r2-Ec-bioC_avg-signal157.235764
Spike_AFFX-r2-Bs-dap_avg-signal86.207489
Spike_AFFX-r2-Bs-dap_3-5-ratio6.356894
Spike_AFFX-r2-Ec-bioB_5_signal53.723408
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.289382
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-11_pen1-3_Bacteria_Root_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Schwochow_590-11_pen1-3_Bacteria_Root_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-11_pen1-3_Bacteria_Root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pen1-3
Stock Code:
Genetic Background: Col-3
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Genetic Variation: EMS induced mutation mutation in AT1G 11310.1
Tissue: roots
in vivo Treatment: - measure OD (around 0,6) - take 2ml „³ centrifuge for 1 minute at 12000rpm - discard supernatant - wash pellet with 10mM MgSO4 „³ centrifuge for 1minute at 12000rpm - discard supernatant - resolve the bacteria pellet in 2ml 10mM MgSO4 - discard tap water from the seeds - bacteria solution to the seeds - incubate for 3 hours - shake slightly every 30 minutes
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.433855
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-ratio1.114242
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.568369
Spike_AFFX-r2-Bs-dap_5_signal67.803391
NoiseAvg:3.18,Std:0.07,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.557871
#P15804
Spike_AFFX-r2-Bs-phe_M_signal29.592009
Corner-Avg:9685,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal69.508568
Spike_AFFX-r2-Ec-bioB_3_signal33.821236
Spike_AFFX-r2-Bs-lys_M_signal20.999001
Spike_AFFX-r2-P1-cre_3_signal2408.828125
Spike_AFFX-r2-Bs-lys_3-5-ratio1.350129
Spike_AFFX-r2-Bs-dap_M_signal213.006516
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.497396
Spike_AFFX-r2-Ec-bioB_avg-signal54.278534
Spike_AFFX-r2-Bs-thr_avg-signal101.802185
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal393.988159
Spike_AFFX-r2-Bs-phe_5_signal33.247753
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal560.972595
RawQ2.955574
Spike_AFFX-r2-Bs-lys_5_signal22.895668
Signal(A)2.932059
%A29.570364
Signal(All)133.764420
Corner+Avg:160,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal196.415970
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal37.387253
Spike_AFFX-r2-Ec-bioD_avg-signal477.480377
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.285400
Spike_AFFX-r2-Bs-lys_avg-signal24.935595
Spike_AFFX-r2-P1-cre_avg-signal2285.341309
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.144235
Spike_AFFX-r2-Bs-thr_3_signal192.049194
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-signal33.409008
Spike_AFFX-r2-Bs-dap_3_signal281.098633
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.423831
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal185.236588
#M261
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.912117
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.060352
Spike_AFFX-r2-Bs-thr_M_signal83.799515
Signal(P)191.618286
Spike_AFFX-r2-Bs-phe_3-5-ratio1.124505
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7180,Count:9
Spike_AFFX-r2-P1-cre_5_signal2161.854492
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6745
Signal(M)11.701179
BackgroundAvg:71.96,Std:0.81,Min:69.8,Max:74.2
Spike_AFFX-r2-Ec-bioC_avg-signal190.826279
Spike_AFFX-r2-Bs-dap_avg-signal187.302856
Spike_AFFX-r2-Bs-dap_3-5-ratio4.145790
Spike_AFFX-r2-Ec-bioB_5_signal59.505795
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.433855
NF1.000000
HZ4
Tau0.015000

Slide: Schwochow_590-12_pen1-3_Bacteria_Root_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("Schwochow_590-12_pen1-3_Bacteria_Root_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Schwochow_590-12_pen1-3_Bacteria_Root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pen1-3
Stock Code:
Genetic Background: Col-3
Age: 33 days
Growth Conditions:
Stratification- before the sterilisation dry seeds stored at 4¢XC in the dark - after sterilisation seeds stored over night in tap water at 4¢XC in the dark
SterilisationSeeds + 1ml 70% Ethanol + 1µl Tween20 Shake for 10 minutes Centrifuge for 1minute at 14000rpm Discard the supernatant Seeds + 1ml 5% NaOCl + 1µl Tween20 Shake for 10 minutes Centrifuge for 1 minute at 14000rpm Discard the supernatant Wash the seeds 5times with sterile water Centrifuge for 1 minute at 14000rpm Seeds + 1ml tap water
Protocol- plants grown on vertical Agar plates - 3-4 seeds per plate - Grown in a growth chamber for 33 days - Light conditions: approximately 130µE;12h light/12h dark - Temperature: day: 18¢XC night: 16¢XC
Percentage Agrose7
Plant Spacing3-4 plants per plate
Temperature17 °C average, 18 °C day, 16 °C night
Humidityestimated 50% % average, estimated 50% % day, estimated 50% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 130µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Genetic Variation: EMS induced mutation mutation in AT1G 11310.1
Tissue: roots
in vivo Treatment: - measure OD (around 0,6) - take 2ml „³ centrifuge for 1 minute at 12000rpm - discard supernatant - wash pellet with 10mM MgSO4 „³ centrifuge for 1minute at 12000rpm - discard supernatant - resolve the bacteria pellet in 2ml 10mM MgSO4 - discard tap water from the seeds - bacteria solution to the seeds - incubate for 3 hours - shake slightly every 30 minutes
Additional Organism Information:
Sample Description- age: 33days old - phenotype: inoculated plants grow significantly higher - roots: grow until the end of the plate
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:0.236853
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-ratio1.149690
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.716223
Spike_AFFX-r2-Bs-dap_5_signal43.936062
NoiseAvg:3.49,Std:0.08,Min:3.2,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.656273
#P16351
Spike_AFFX-r2-Bs-phe_M_signal17.638775
Corner-Avg:11154,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal47.547272
Spike_AFFX-r2-Ec-bioB_3_signal28.800007
Spike_AFFX-r2-Bs-lys_M_signal15.454460
Spike_AFFX-r2-P1-cre_3_signal1959.165039
Spike_AFFX-r2-Bs-lys_3-5-ratio2.053356
Spike_AFFX-r2-Bs-dap_M_signal117.685699
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.521502
Spike_AFFX-r2-Ec-bioB_avg-signal38.852749
Spike_AFFX-r2-Bs-thr_avg-signal51.328339
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal322.323944
Spike_AFFX-r2-Bs-phe_5_signal22.795866
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal453.347931
RawQ2.949986
Spike_AFFX-r2-Bs-lys_5_signal13.860013
Signal(A)1.924092
%A27.088997
Signal(All)129.078522
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal142.318787
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.850796
Spike_AFFX-r2-Ec-bioD_avg-signal387.835938
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.683472
Spike_AFFX-r2-Bs-lys_avg-signal19.258001
Spike_AFFX-r2-P1-cre_avg-signal1831.622925
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.227532
Spike_AFFX-r2-Bs-thr_3_signal88.875885
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-signal21.428480
Spike_AFFX-r2-Bs-dap_3_signal202.333267
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.406498
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal131.755814
#M280
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.459536
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.080171
Spike_AFFX-r2-Bs-thr_M_signal45.452843
Signal(P)179.203125
Spike_AFFX-r2-Bs-phe_3-5-ratio1.046277
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8984,Count:9
Spike_AFFX-r2-P1-cre_5_signal1704.080811
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6179
Signal(M)8.006650
BackgroundAvg:74.70,Std:0.86,Min:71.8,Max:77.5
Spike_AFFX-r2-Ec-bioC_avg-signal137.037292
Spike_AFFX-r2-Bs-dap_avg-signal121.318352
Spike_AFFX-r2-Bs-dap_3-5-ratio4.605175
Spike_AFFX-r2-Ec-bioB_5_signal40.210976
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.236853
NF1.000000
HZ4
Tau0.015000


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