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Experiment: Changes in genome of selected lines in comparison to wildtype

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-553

The aim of this microarray analysis is to analyse whole-genome changes in plants altered in the expression and/or activity of CESTA (CES), a transcription factor involved in the regulation of brassinosteroid responses.The lines analysed are the dominant mutant ces-D, and plants constitutively expressing a dominant negative version of CES (CES-SRDX) as compared to those of wild-type. The tissues used were ten-day-old whole seedlings grown in long-day conditions at 22°C.

About the Experimenter

Name: Mamoona Khan
Head of Lab Name: Brigitte Poppenberger
Lab:
Address:Department of Plant Molecular Biology, Centre for Molecular Biology, University of Vienna
Dr. Bohr-Gasse 9, Wien, Vienna, , A-1030, AUSTRIA
Postcode:
Country:
 
Telephone Number: 00431487774610

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

About this Experiment

Experiment Type: genetic_modification_design
Number of Slides:9
 
Experimental Parameters:
parametergenetic_modification
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Khan: Changes in genome of selected lines in comparison to wildtype

Slide: Khan_553-1_Col-0_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 ("Khan_553-1_Col-0_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: Khan_553-1_Col-0_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.478672
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-ratio1.247132
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.113022
Spike_AFFX-r2-Bs-dap_5_signal65.212700
NoiseAvg:2.21,Std:0.06,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.102695
#P16145
Spike_AFFX-r2-Bs-phe_M_signal22.876099
Corner-Avg:7572,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.356606
Spike_AFFX-r2-Ec-bioB_3_signal76.974152
Spike_AFFX-r2-Bs-lys_M_signal9.483397
Spike_AFFX-r2-P1-cre_3_signal4357.579590
Spike_AFFX-r2-Bs-lys_3-5-ratio3.350777
Spike_AFFX-r2-Bs-dap_M_signal169.309509
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.144495
Spike_AFFX-r2-Ec-bioB_avg-signal78.829521
Spike_AFFX-r2-Bs-thr_avg-signal52.879822
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal834.880432
Spike_AFFX-r2-Bs-phe_5_signal31.851429
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1106.278931
RawQ1.982634
Spike_AFFX-r2-Bs-lys_5_signal12.848989
Signal(A)3.159999
%A27.821131
Signal(All)137.934845
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal266.773346
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal38.087311
Spike_AFFX-r2-Ec-bioD_avg-signal970.579712
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.780357
Spike_AFFX-r2-Bs-lys_avg-signal21.795496
Spike_AFFX-r2-P1-cre_avg-signal3925.830078
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.398509
Spike_AFFX-r2-Bs-thr_3_signal78.935295
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal30.938278
Spike_AFFX-r2-Bs-dap_3_signal216.823669
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.325075
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal284.780792
#M319
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.054100
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.936767
Spike_AFFX-r2-Bs-thr_M_signal54.601471
Signal(P)193.402573
Spike_AFFX-r2-Bs-phe_3-5-ratio1.195780
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6037,Count:9
Spike_AFFX-r2-P1-cre_5_signal3494.080566
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6346
Signal(M)11.774430
BackgroundAvg:47.67,Std:0.59,Min:46.4,Max:49.1
Spike_AFFX-r2-Ec-bioC_avg-signal275.777069
Spike_AFFX-r2-Bs-dap_avg-signal150.448624
Spike_AFFX-r2-Bs-dap_3-5-ratio3.324869
Spike_AFFX-r2-Ec-bioB_5_signal69.157814
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.478672
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-2_Col-0_Rep_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 ("Khan_553-2_Col-0_Rep_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: Khan_553-2_Col-0_Rep_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.557756
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-ratio1.226178
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.856279
Spike_AFFX-r2-Bs-dap_5_signal64.457428
NoiseAvg:2.34,Std:0.10,Min:2.1,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.425028
#P15834
Spike_AFFX-r2-Bs-phe_M_signal21.630692
Corner-Avg:7749,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal104.060654
Spike_AFFX-r2-Ec-bioB_3_signal77.137085
Spike_AFFX-r2-Bs-lys_M_signal12.365273
Spike_AFFX-r2-P1-cre_3_signal4867.433105
Spike_AFFX-r2-Bs-lys_3-5-ratio1.780164
Spike_AFFX-r2-Bs-dap_M_signal159.746689
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.355064
Spike_AFFX-r2-Ec-bioB_avg-signal90.427269
Spike_AFFX-r2-Bs-thr_avg-signal50.348511
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal974.389343
Spike_AFFX-r2-Bs-phe_5_signal26.232821
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1467.468506
RawQ2.205065
Spike_AFFX-r2-Bs-lys_5_signal19.296232
Signal(A)3.746392
%A29.031126
Signal(All)139.517502
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal338.358978
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.569500
Spike_AFFX-r2-Ec-bioD_avg-signal1220.928955
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.416924
Spike_AFFX-r2-Bs-lys_avg-signal22.003984
Spike_AFFX-r2-P1-cre_avg-signal4418.515137
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.551951
Spike_AFFX-r2-Bs-thr_3_signal69.297829
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.144339
Spike_AFFX-r2-Bs-dap_3_signal194.171280
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.506039
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal342.723328
#M354
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.350449
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.987266
Spike_AFFX-r2-Bs-thr_M_signal52.322670
Signal(P)199.093704
Spike_AFFX-r2-Bs-phe_3-5-ratio0.822233
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5985,Count:9
Spike_AFFX-r2-P1-cre_5_signal3969.597412
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6622
Signal(M)14.507587
BackgroundAvg:52.53,Std:0.46,Min:51.3,Max:53.9
Spike_AFFX-r2-Ec-bioC_avg-signal340.541138
Spike_AFFX-r2-Bs-dap_avg-signal139.458466
Spike_AFFX-r2-Bs-dap_3-5-ratio3.012396
Spike_AFFX-r2-Ec-bioB_5_signal90.084045
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.557756
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-3_Col-0_Rep_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 ("Khan_553-3_Col-0_Rep_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: Khan_553-3_Col-0_Rep_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.573655
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-ratio1.123545
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.855482
Spike_AFFX-r2-Bs-dap_5_signal65.958496
NoiseAvg:2.40,Std:0.07,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.671755
#P15850
Spike_AFFX-r2-Bs-phe_M_signal24.189976
Corner-Avg:8448,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal104.281509
Spike_AFFX-r2-Ec-bioB_3_signal72.123817
Spike_AFFX-r2-Bs-lys_M_signal12.196003
Spike_AFFX-r2-P1-cre_3_signal4445.615723
Spike_AFFX-r2-Bs-lys_3-5-ratio1.730035
Spike_AFFX-r2-Bs-dap_M_signal188.071228
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.173528
Spike_AFFX-r2-Ec-bioB_avg-signal86.904381
Spike_AFFX-r2-Bs-thr_avg-signal52.433483
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal845.237366
Spike_AFFX-r2-Bs-phe_5_signal25.195793
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1440.110596
RawQ2.228475
Spike_AFFX-r2-Bs-lys_5_signal15.062636
Signal(A)3.719680
%A28.917141
Signal(All)139.869568
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal331.548676
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.463318
Spike_AFFX-r2-Ec-bioD_avg-signal1142.673950
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.487068
Spike_AFFX-r2-Bs-lys_avg-signal17.772512
Spike_AFFX-r2-P1-cre_avg-signal4201.195313
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.595791
Spike_AFFX-r2-Bs-thr_3_signal78.296501
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-signal22.949697
Spike_AFFX-r2-Bs-dap_3_signal216.693130
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.703794
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal320.206207
#M364
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.058895
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.035422
Spike_AFFX-r2-Bs-thr_M_signal54.332195
Signal(P)199.423096
Spike_AFFX-r2-Bs-phe_3-5-ratio0.772483
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5662,Count:9
Spike_AFFX-r2-P1-cre_5_signal3956.774414
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6596
Signal(M)13.828797
BackgroundAvg:53.17,Std:0.51,Min:52.0,Max:54.4
Spike_AFFX-r2-Ec-bioC_avg-signal325.877441
Spike_AFFX-r2-Bs-dap_avg-signal156.907608
Spike_AFFX-r2-Bs-dap_3-5-ratio3.285295
Spike_AFFX-r2-Ec-bioB_5_signal84.307816
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.573655
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-4_ces-D_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Khan_553-4_ces-D_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: Khan_553-4_ces-D_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: cesD
Stock Code:
Genetic Background: Col-0
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: Enhancer Trap knock out mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.537257
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-ratio1.033370
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.029048
Spike_AFFX-r2-Bs-dap_5_signal54.926292
NoiseAvg:2.22,Std:0.08,Min:2.1,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.970949
#P15730
Spike_AFFX-r2-Bs-phe_M_signal21.511166
Corner-Avg:7351,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.556976
Spike_AFFX-r2-Ec-bioB_3_signal56.382027
Spike_AFFX-r2-Bs-lys_M_signal13.954181
Spike_AFFX-r2-P1-cre_3_signal3364.608887
Spike_AFFX-r2-Bs-lys_3-5-ratio2.064294
Spike_AFFX-r2-Bs-dap_M_signal134.115372
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.457035
Spike_AFFX-r2-Ec-bioB_avg-signal59.909832
Spike_AFFX-r2-Bs-thr_avg-signal53.248623
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal632.907715
Spike_AFFX-r2-Bs-phe_5_signal20.195656
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1177.275513
RawQ2.068840
Spike_AFFX-r2-Bs-lys_5_signal13.691688
Signal(A)3.340985
%A29.526524
Signal(All)138.439484
Corner+Avg:104,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal251.508591
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.311789
Spike_AFFX-r2-Ec-bioD_avg-signal905.091614
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.960983
Spike_AFFX-r2-Bs-lys_avg-signal18.636513
Spike_AFFX-r2-P1-cre_avg-signal3310.283691
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal82.868401
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-signal21.006203
Spike_AFFX-r2-Bs-dap_3_signal164.000107
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.860106
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal227.077820
#M345
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.263670
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.107588
Spike_AFFX-r2-Bs-thr_M_signal52.906521
Signal(P)199.013718
Spike_AFFX-r2-Bs-phe_3-5-ratio1.055266
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4782,Count:9
Spike_AFFX-r2-P1-cre_5_signal3255.958252
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6735
Signal(M)13.963689
BackgroundAvg:49.66,Std:0.41,Min:48.5,Max:50.7
Spike_AFFX-r2-Ec-bioC_avg-signal239.293213
Spike_AFFX-r2-Bs-dap_avg-signal117.680595
Spike_AFFX-r2-Bs-dap_3-5-ratio2.985821
Spike_AFFX-r2-Ec-bioB_5_signal54.790485
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.537257
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-5_ces-D_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 ("Khan_553-5_ces-D_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: Khan_553-5_ces-D_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: cesD
Stock Code:
Genetic Background: Col-0
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: Enhancer Trap knock out mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.864294
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-ratio1.210277
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.839047
Spike_AFFX-r2-Bs-dap_5_signal55.834400
NoiseAvg:2.03,Std:0.05,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.354782
#P15404
Spike_AFFX-r2-Bs-phe_M_signal20.799871
Corner-Avg:8288,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal109.047508
Spike_AFFX-r2-Ec-bioB_3_signal89.267715
Spike_AFFX-r2-Bs-lys_M_signal11.794477
Spike_AFFX-r2-P1-cre_3_signal5493.654785
Spike_AFFX-r2-Bs-lys_3-5-ratio1.676049
Spike_AFFX-r2-Bs-dap_M_signal93.478180
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.239863
Spike_AFFX-r2-Ec-bioB_avg-signal101.569023
Spike_AFFX-r2-Bs-thr_avg-signal33.287251
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal973.797363
Spike_AFFX-r2-Bs-phe_5_signal17.785254
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1484.271606
RawQ1.941639
Spike_AFFX-r2-Bs-lys_5_signal15.578015
Signal(A)4.493797
%A30.736519
Signal(All)142.760147
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal385.570984
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.091202
Spike_AFFX-r2-Ec-bioD_avg-signal1229.034424
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.531784
Spike_AFFX-r2-Bs-lys_avg-signal17.827337
Spike_AFFX-r2-P1-cre_avg-signal5016.413086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.731697
Spike_AFFX-r2-Bs-thr_3_signal28.956738
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-signal19.558777
Spike_AFFX-r2-Bs-dap_3_signal153.601196
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.524210
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal359.300446
#M395
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.109522
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.073116
Spike_AFFX-r2-Bs-thr_M_signal47.550232
Signal(P)208.936798
Spike_AFFX-r2-Bs-phe_3-5-ratio1.129655
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5812,Count:9
Spike_AFFX-r2-P1-cre_5_signal4539.171387
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7011
Signal(M)16.178352
BackgroundAvg:49.14,Std:0.44,Min:47.9,Max:50.1
Spike_AFFX-r2-Ec-bioC_avg-signal372.435730
Spike_AFFX-r2-Bs-dap_avg-signal100.971260
Spike_AFFX-r2-Bs-dap_3-5-ratio2.751014
Spike_AFFX-r2-Ec-bioB_5_signal106.391846
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.864294
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-6_ces-D_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 ("Khan_553-6_ces-D_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: Khan_553-6_ces-D_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: cesD
Stock Code:
Genetic Background: Col-0
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: Enhancer Trap knock out mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.677434
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-ratio1.004066
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.928753
Spike_AFFX-r2-Bs-dap_5_signal62.587521
NoiseAvg:2.33,Std:0.10,Min:2.0,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal26.000616
#P15494
Spike_AFFX-r2-Bs-phe_M_signal22.806305
Corner-Avg:8585,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal95.414406
Spike_AFFX-r2-Ec-bioB_3_signal81.912216
Spike_AFFX-r2-Bs-lys_M_signal12.062476
Spike_AFFX-r2-P1-cre_3_signal3878.225098
Spike_AFFX-r2-Bs-lys_3-5-ratio1.681295
Spike_AFFX-r2-Bs-dap_M_signal135.210693
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.638900
Spike_AFFX-r2-Ec-bioB_avg-signal88.507507
Spike_AFFX-r2-Bs-thr_avg-signal40.452793
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal755.983582
Spike_AFFX-r2-Bs-phe_5_signal19.846380
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1429.336304
RawQ2.125251
Spike_AFFX-r2-Bs-lys_5_signal14.668187
Signal(A)4.392896
%A30.486629
Signal(All)140.988922
Corner+Avg:113,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal359.288635
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.747807
Spike_AFFX-r2-Ec-bioD_avg-signal1092.659912
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.926346
Spike_AFFX-r2-Bs-lys_avg-signal17.130739
Spike_AFFX-r2-P1-cre_avg-signal3870.373047
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.587023
Spike_AFFX-r2-Bs-thr_3_signal42.612404
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.800163
Spike_AFFX-r2-Bs-dap_3_signal183.469315
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.890698
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal312.054291
#M362
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.661556
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.151366
Spike_AFFX-r2-Bs-thr_M_signal52.745358
Signal(P)205.221527
Spike_AFFX-r2-Bs-phe_3-5-ratio1.448516
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6805,Count:9
Spike_AFFX-r2-P1-cre_5_signal3862.521240
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6954
Signal(M)15.765099
BackgroundAvg:53.01,Std:0.33,Min:52.2,Max:54.0
Spike_AFFX-r2-Ec-bioC_avg-signal335.671448
Spike_AFFX-r2-Bs-dap_avg-signal127.089172
Spike_AFFX-r2-Bs-dap_3-5-ratio2.931404
Spike_AFFX-r2-Ec-bioB_5_signal88.195908
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.677434
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-7_203_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Khan_553-7_203_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: Khan_553-7_203_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ces dominant negative
Stock Code:
Genetic Background: Col-0
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.759042
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-ratio0.954887
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.964869
Spike_AFFX-r2-Bs-dap_5_signal65.501923
NoiseAvg:2.04,Std:0.07,Min:1.9,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.680367
#P15684
Spike_AFFX-r2-Bs-phe_M_signal16.302338
Corner-Avg:7672,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal113.275627
Spike_AFFX-r2-Ec-bioB_3_signal79.314941
Spike_AFFX-r2-Bs-lys_M_signal13.849654
Spike_AFFX-r2-P1-cre_3_signal4240.128906
Spike_AFFX-r2-Bs-lys_3-5-ratio1.829337
Spike_AFFX-r2-Bs-dap_M_signal117.326591
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.713626
Spike_AFFX-r2-Ec-bioB_avg-signal91.597801
Spike_AFFX-r2-Bs-thr_avg-signal41.209110
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal787.698059
Spike_AFFX-r2-Bs-phe_5_signal16.819939
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1295.413574
RawQ1.952209
Spike_AFFX-r2-Bs-lys_5_signal8.900102
Signal(A)4.003987
%A29.719421
Signal(All)141.338303
Corner+Avg:94,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal340.731323
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.054484
Spike_AFFX-r2-Ec-bioD_avg-signal1041.555786
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.759315
Spike_AFFX-r2-Bs-lys_avg-signal13.010346
Spike_AFFX-r2-P1-cre_avg-signal4340.290039
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.521263
Spike_AFFX-r2-Bs-thr_3_signal61.944637
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-signal15.725587
Spike_AFFX-r2-Bs-dap_3_signal165.553513
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.644556
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal296.819031
#M347
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.281284
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.147943
Spike_AFFX-r2-Bs-thr_M_signal45.002323
Signal(P)203.481583
Spike_AFFX-r2-Bs-phe_3-5-ratio0.835585
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5841,Count:9
Spike_AFFX-r2-P1-cre_5_signal4440.450684
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6779
Signal(M)15.500098
BackgroundAvg:50.45,Std:0.60,Min:48.9,Max:51.7
Spike_AFFX-r2-Ec-bioC_avg-signal318.775177
Spike_AFFX-r2-Bs-dap_avg-signal116.127342
Spike_AFFX-r2-Bs-dap_3-5-ratio2.527460
Spike_AFFX-r2-Ec-bioB_5_signal82.202812
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.759042
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-8_203_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 ("Khan_553-8_203_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: Khan_553-8_203_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ces dominant negative
Stock Code:
Genetic Background: Col-0
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.663993
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-ratio1.226465
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.926169
Spike_AFFX-r2-Bs-dap_5_signal65.954559
NoiseAvg:2.23,Std:0.06,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.226656
#P15633
Spike_AFFX-r2-Bs-phe_M_signal17.047323
Corner-Avg:7832,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal109.594948
Spike_AFFX-r2-Ec-bioB_3_signal66.319199
Spike_AFFX-r2-Bs-lys_M_signal9.912431
Spike_AFFX-r2-P1-cre_3_signal5006.735352
Spike_AFFX-r2-Bs-lys_3-5-ratio1.682482
Spike_AFFX-r2-Bs-dap_M_signal150.483612
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.316381
Spike_AFFX-r2-Ec-bioB_avg-signal82.506706
Spike_AFFX-r2-Bs-thr_avg-signal52.687347
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal868.307861
Spike_AFFX-r2-Bs-phe_5_signal22.810001
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1358.098389
RawQ2.203455
Spike_AFFX-r2-Bs-lys_5_signal9.438452
Signal(A)4.045982
%A29.837790
Signal(All)139.345276
Corner+Avg:104,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal361.358398
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.195084
Spike_AFFX-r2-Ec-bioD_avg-signal1113.203125
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.535728
Spike_AFFX-r2-Bs-lys_avg-signal11.743637
Spike_AFFX-r2-P1-cre_avg-signal4544.492188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal67.700073
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-signal20.684137
Spike_AFFX-r2-Bs-dap_3_signal166.672577
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.564075
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal349.275787
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.880030
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.034593
Spike_AFFX-r2-Bs-thr_M_signal61.135307
Signal(P)201.203735
Spike_AFFX-r2-Bs-phe_3-5-ratio0.973042
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5523,Count:9
Spike_AFFX-r2-P1-cre_5_signal4082.249023
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6806
Signal(M)14.853960
BackgroundAvg:51.84,Std:0.45,Min:50.6,Max:53.3
Spike_AFFX-r2-Ec-bioC_avg-signal355.317078
Spike_AFFX-r2-Bs-dap_avg-signal127.703583
Spike_AFFX-r2-Bs-dap_3-5-ratio2.527082
Spike_AFFX-r2-Ec-bioB_5_signal71.605949
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.663993
NF1.000000
HZ4
Tau0.015000

Slide: Khan_553-9_203_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 ("Khan_553-9_203_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: Khan_553-9_203_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: ces dominant negative
Stock Code:
Genetic Background: Col-0
Age: 10.3 days
Growth Conditions:
ProtocolThe seedlings were grown on Agar plates under long day conditions at 22°C for 10 days.
Percentage Agrose10
Temperature22°C °C average, 22°C °C day, 22°C °C night
Humidity38% % average, 38% % day, 38% % night
MediumOwn medium:
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.736294
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-ratio1.266537
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.044349
Spike_AFFX-r2-Bs-dap_5_signal41.432205
NoiseAvg:2.02,Std:0.08,Min:1.8,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.706345
#P15576
Spike_AFFX-r2-Bs-phe_M_signal10.924630
Corner-Avg:7107,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal97.499435
Spike_AFFX-r2-Ec-bioB_3_signal64.589622
Spike_AFFX-r2-Bs-lys_M_signal6.598721
Spike_AFFX-r2-P1-cre_3_signal4540.914551
Spike_AFFX-r2-Bs-lys_3-5-ratio1.260730
Spike_AFFX-r2-Bs-dap_M_signal93.370621
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.964738
Spike_AFFX-r2-Ec-bioB_avg-signal74.645271
Spike_AFFX-r2-Bs-thr_avg-signal35.455395
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal724.217896
Spike_AFFX-r2-Bs-phe_5_signal18.491428
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1137.788940
RawQ2.010018
Spike_AFFX-r2-Bs-lys_5_signal17.147860
Signal(A)4.143744
%A29.991232
Signal(All)139.986832
Corner+Avg:94,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal274.569244
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.029776
Spike_AFFX-r2-Ec-bioD_avg-signal931.003418
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.285843
Spike_AFFX-r2-Bs-lys_avg-signal15.121800
Spike_AFFX-r2-P1-cre_avg-signal4063.107422
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal44.612026
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-signal15.815278
Spike_AFFX-r2-Bs-dap_3_signal108.841774
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.571059
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal269.445435
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.618824
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.019016
Spike_AFFX-r2-Bs-thr_M_signal39.047806
Signal(P)202.804550
Spike_AFFX-r2-Bs-phe_3-5-ratio0.975034
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4922,Count:9
Spike_AFFX-r2-P1-cre_5_signal3585.300049
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6841
Signal(M)14.932589
BackgroundAvg:47.70,Std:0.50,Min:46.6,Max:48.9
Spike_AFFX-r2-Ec-bioC_avg-signal272.007324
Spike_AFFX-r2-Bs-dap_avg-signal81.214867
Spike_AFFX-r2-Bs-dap_3-5-ratio2.626985
Spike_AFFX-r2-Ec-bioB_5_signal61.846775
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.736294
NF1.000000
HZ4
Tau0.015000


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