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Experiment: whole genome analysis

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-598

The aim of this microarray analysis is to analyse whole-genome changes in plants in which the expression of a transcription factor involved in the regulation of brassinosteroid homeostasis is induced.The lines analysed expressed a TF under inducible promoter as compared to those of wild-type. The tissues used were ten-day-old whole seedlings grown in the light at 22°C.

About the Experimenter

Name: Mamoona Khan
Head of Lab Name: Brigitte Poppenberger
Lab:
Address:Department of Plant Molecular Biology (Account ATU57...68), Centre for Molecular Biology, University of Vienna
Dr. Bohr-Gasse 9, Wien, Vienna, , A-1030, AUSTRIA
Postcode: A-1030
Country: AUSTRIA
 
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: gene_knock_in
Number of Slides:18
 
Experimental Parameters:
parametergene_knock_in
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Khan: whole genome analysis

Slide: Khan_598-1_Col0-1-Control_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_598-1_Col0-1-Control_Rep1_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-1_Col0-1-Control_Rep1_ATH1
Organism:
Stock Code:
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:0.328426
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-ratio1.337121
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.072939
Spike_AFFX-r2-Bs-dap_5_signal177.890381
NoiseAvg:3.12,Std:0.10,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal49.030525
#P16668
Spike_AFFX-r2-Bs-phe_M_signal54.680523
Corner-Avg:12087,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal47.803680
Spike_AFFX-r2-Ec-bioB_3_signal33.766754
Spike_AFFX-r2-Bs-lys_M_signal28.601778
Spike_AFFX-r2-P1-cre_3_signal2358.328613
Spike_AFFX-r2-Bs-lys_3-5-ratio1.632759
Spike_AFFX-r2-Bs-dap_M_signal338.445618
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.320652
Spike_AFFX-r2-Ec-bioB_avg-signal37.680569
Spike_AFFX-r2-Bs-thr_avg-signal109.836548
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal335.825470
Spike_AFFX-r2-Bs-phe_5_signal85.020462
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal518.052002
RawQ2.604852
Spike_AFFX-r2-Bs-lys_5_signal37.722878
Signal(A)2.655048
%A25.786936
Signal(All)128.027969
Corner+Avg:198,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal111.581642
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal89.730797
Spike_AFFX-r2-Ec-bioD_avg-signal426.938721
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P73.073212
Spike_AFFX-r2-Bs-lys_avg-signal42.639011
Spike_AFFX-r2-P1-cre_avg-signal2061.032227
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.139851
Spike_AFFX-r2-Bs-thr_3_signal162.813339
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-signal76.477257
Spike_AFFX-r2-Bs-dap_3_signal521.726135
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.542623
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal105.373665
#M260
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.592377
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.058914
Spike_AFFX-r2-Bs-thr_M_signal117.665794
Signal(P)174.101654
Spike_AFFX-r2-Bs-phe_3-5-ratio1.055402
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10389,Count:9
Spike_AFFX-r2-P1-cre_5_signal1763.735840
Spike_AFFX-r2-Bs-phe_M_detectionP
#A5882
Signal(M)10.672218
BackgroundAvg:58.47,Std:0.48,Min:56.7,Max:59.7
Spike_AFFX-r2-Ec-bioC_avg-signal108.477654
Spike_AFFX-r2-Bs-dap_avg-signal346.020721
Spike_AFFX-r2-Bs-dap_3-5-ratio2.932852
Spike_AFFX-r2-Ec-bioB_5_signal31.471275
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.328426
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-2_Col0-1-Control_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_598-2_Col0-1-Control_Rep2_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-2_Col0-1-Control_Rep2_ATH1
Organism:
Stock Code:
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:0.427838
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-ratio1.374332
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.955087
Spike_AFFX-r2-Bs-dap_5_signal92.658371
NoiseAvg:3.45,Std:0.12,Min:3.2,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal36.307602
#P16039
Spike_AFFX-r2-Bs-phe_M_signal40.713928
Corner-Avg:10362,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal43.365330
Spike_AFFX-r2-Ec-bioB_3_signal39.145679
Spike_AFFX-r2-Bs-lys_M_signal17.892538
Spike_AFFX-r2-P1-cre_3_signal2219.155273
Spike_AFFX-r2-Bs-lys_3-5-ratio0.881038
Spike_AFFX-r2-Bs-dap_M_signal200.521790
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.049999
Spike_AFFX-r2-Ec-bioB_avg-signal41.165844
Spike_AFFX-r2-Bs-thr_avg-signal73.497505
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal332.307495
Spike_AFFX-r2-Bs-phe_5_signal40.001858
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal488.088684
RawQ3.004276
Spike_AFFX-r2-Bs-lys_5_signal31.305752
Signal(A)3.364425
%A28.268303
Signal(All)129.815521
Corner+Avg:177,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal113.473289
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal49.424519
Spike_AFFX-r2-Ec-bioD_avg-signal410.198090
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.315651
Spike_AFFX-r2-Bs-lys_avg-signal25.593285
Spike_AFFX-r2-P1-cre_avg-signal1916.935303
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.416046
Spike_AFFX-r2-Bs-thr_3_signal110.738167
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-signal43.380100
Spike_AFFX-r2-Bs-dap_3_signal280.365936
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.468786
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal102.751358
#M323
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.581564
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.104348
Spike_AFFX-r2-Bs-thr_M_signal73.446747
Signal(P)183.022736
Spike_AFFX-r2-Bs-phe_3-5-ratio1.235556
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8861,Count:9
Spike_AFFX-r2-P1-cre_5_signal1614.715454
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6448
Signal(M)12.062961
BackgroundAvg:67.56,Std:1.43,Min:63.9,Max:71.4
Spike_AFFX-r2-Ec-bioC_avg-signal108.112320
Spike_AFFX-r2-Bs-dap_avg-signal191.182022
Spike_AFFX-r2-Bs-dap_3-5-ratio3.025803
Spike_AFFX-r2-Ec-bioB_5_signal40.986515
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.427838
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-3_Col0-1-Control_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_598-3_Col0-1-Control_Rep3_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-3_Col0-1-Control_Rep3_ATH1
Organism:
Stock Code:
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:0.360748
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-ratio1.146096
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.844570
Spike_AFFX-r2-Bs-dap_5_signal152.193695
NoiseAvg:3.17,Std:0.11,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_signal49.108639
#P16547
Spike_AFFX-r2-Bs-phe_M_signal43.750931
Corner-Avg:11798,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal41.588455
Spike_AFFX-r2-Ec-bioB_3_signal27.685429
Spike_AFFX-r2-Bs-lys_M_signal24.887928
Spike_AFFX-r2-P1-cre_3_signal2005.104492
Spike_AFFX-r2-Bs-lys_3-5-ratio1.424078
Spike_AFFX-r2-Bs-dap_M_signal295.209686
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.501284
Spike_AFFX-r2-Ec-bioB_avg-signal34.018127
Spike_AFFX-r2-Bs-thr_avg-signal94.031883
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal293.029633
Spike_AFFX-r2-Bs-phe_5_signal64.633385
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal468.338165
RawQ2.806777
Spike_AFFX-r2-Bs-lys_5_signal39.553448
Signal(A)2.594219
%A26.391933
Signal(All)128.865021
Corner+Avg:188,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal109.022888
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal68.087639
Spike_AFFX-r2-Ec-bioD_avg-signal380.683899
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P72.542747
Spike_AFFX-r2-Bs-lys_avg-signal40.256195
Spike_AFFX-r2-P1-cre_avg-signal1877.306396
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.065322
Spike_AFFX-r2-Bs-thr_3_signal122.834671
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-signal58.823986
Spike_AFFX-r2-Bs-dap_3_signal432.140930
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.598262
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal99.753090
#M243
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.327206
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.092927
Spike_AFFX-r2-Bs-thr_M_signal110.152321
Signal(P)176.544785
Spike_AFFX-r2-Bs-phe_3-5-ratio1.053444
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9900,Count:9
Spike_AFFX-r2-P1-cre_5_signal1749.508423
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6020
Signal(M)10.319313
BackgroundAvg:66.74,Std:0.66,Min:65.4,Max:68.9
Spike_AFFX-r2-Ec-bioC_avg-signal104.387985
Spike_AFFX-r2-Bs-dap_avg-signal293.181427
Spike_AFFX-r2-Bs-dap_3-5-ratio2.839414
Spike_AFFX-r2-Ec-bioB_5_signal32.780502
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.360748
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-4_Col0-1-6h_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_598-4_Col0-1-6h_Rep1_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-4_Col0-1-6h_Rep1_ATH1
Organism:
Stock Code:
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:0.418523
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-ratio1.376763
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.928878
Spike_AFFX-r2-Bs-dap_5_signal178.627182
NoiseAvg:2.88,Std:0.09,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal56.232853
#P16231
Spike_AFFX-r2-Bs-phe_M_signal56.730350
Corner-Avg:11874,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal43.608070
Spike_AFFX-r2-Ec-bioB_3_signal28.605465
Spike_AFFX-r2-Bs-lys_M_signal34.117977
Spike_AFFX-r2-P1-cre_3_signal2407.262451
Spike_AFFX-r2-Bs-lys_3-5-ratio1.298779
Spike_AFFX-r2-Bs-dap_M_signal361.000702
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.146299
Spike_AFFX-r2-Ec-bioB_avg-signal34.336414
Spike_AFFX-r2-Bs-thr_avg-signal140.576675
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal343.113525
Spike_AFFX-r2-Bs-phe_5_signal81.268326
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal522.594910
RawQ2.547328
Spike_AFFX-r2-Bs-lys_5_signal54.712719
Signal(A)2.731773
%A27.483561
Signal(All)130.498581
Corner+Avg:188,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal108.330177
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal77.731400
Spike_AFFX-r2-Ec-bioD_avg-signal432.854218
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.157387
Spike_AFFX-r2-Bs-lys_avg-signal53.296803
Spike_AFFX-r2-P1-cre_avg-signal2077.878662
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.359053
Spike_AFFX-r2-Bs-thr_3_signal233.158203
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-signal71.910027
Spike_AFFX-r2-Bs-dap_3_signal551.481934
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.523096
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal103.371819
#M310
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal71.059715
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.047966
Spike_AFFX-r2-Bs-thr_M_signal132.338989
Signal(P)182.134430
Spike_AFFX-r2-Bs-phe_3-5-ratio0.956478
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9238,Count:9
Spike_AFFX-r2-P1-cre_5_signal1748.494873
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6269
Signal(M)10.719422
BackgroundAvg:61.79,Std:0.66,Min:59.7,Max:63.8
Spike_AFFX-r2-Ec-bioC_avg-signal105.850998
Spike_AFFX-r2-Bs-dap_avg-signal363.703278
Spike_AFFX-r2-Bs-dap_3-5-ratio3.087335
Spike_AFFX-r2-Ec-bioB_5_signal30.795719
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.418523
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-5_Col0-1-6h_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_598-5_Col0-1-6h_Rep2_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-5_Col0-1-6h_Rep2_ATH1
Organism:
Stock Code:
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:0.378806
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-ratio1.536828
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.786321
Spike_AFFX-r2-Bs-dap_5_signal113.300774
NoiseAvg:3.02,Std:0.09,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.747177
#P16508
Spike_AFFX-r2-Bs-phe_M_signal25.721039
Corner-Avg:10946,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal40.668549
Spike_AFFX-r2-Ec-bioB_3_signal27.685417
Spike_AFFX-r2-Bs-lys_M_signal16.700895
Spike_AFFX-r2-P1-cre_3_signal2188.055176
Spike_AFFX-r2-Bs-lys_3-5-ratio1.411057
Spike_AFFX-r2-Bs-dap_M_signal212.487152
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.883361
Spike_AFFX-r2-Ec-bioB_avg-signal34.520924
Spike_AFFX-r2-Bs-thr_avg-signal62.323505
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal291.459778
Spike_AFFX-r2-Bs-phe_5_signal42.163708
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal407.207886
RawQ2.713287
Spike_AFFX-r2-Bs-lys_5_signal19.167658
Signal(A)2.554188
%A26.457693
Signal(All)128.267487
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal101.254929
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.768028
Spike_AFFX-r2-Ec-bioD_avg-signal349.333832
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P72.371765
Spike_AFFX-r2-Bs-lys_avg-signal20.971733
Spike_AFFX-r2-P1-cre_avg-signal1805.901245
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.170539
Spike_AFFX-r2-Bs-thr_3_signal88.655212
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal38.217590
Spike_AFFX-r2-Bs-dap_3_signal311.509186
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.397132
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal84.344505
#M267
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.046648
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.200492
Spike_AFFX-r2-Bs-thr_M_signal67.568130
Signal(P)176.135010
Spike_AFFX-r2-Bs-phe_3-5-ratio1.109201
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9837,Count:9
Spike_AFFX-r2-P1-cre_5_signal1423.747314
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6035
Signal(M)10.224903
BackgroundAvg:65.20,Std:0.73,Min:62.7,Max:66.7
Spike_AFFX-r2-Ec-bioC_avg-signal92.799713
Spike_AFFX-r2-Bs-dap_avg-signal212.432373
Spike_AFFX-r2-Bs-dap_3-5-ratio2.749400
Spike_AFFX-r2-Ec-bioB_5_signal35.208805
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.378806
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-6_Col0-1-6h_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_598-6_Col0-1-6h_Rep3_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-6_Col0-1-6h_Rep3_ATH1
Organism:
Stock Code:
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:0.521266
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-ratio1.565629
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.746674
Spike_AFFX-r2-Bs-dap_5_signal132.239105
NoiseAvg:2.85,Std:0.10,Min:2.4,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal36.884007
#P16055
Spike_AFFX-r2-Bs-phe_M_signal44.429932
Corner-Avg:7633,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal40.349491
Spike_AFFX-r2-Ec-bioB_3_signal29.193155
Spike_AFFX-r2-Bs-lys_M_signal32.485985
Spike_AFFX-r2-P1-cre_3_signal2828.368164
Spike_AFFX-r2-Bs-lys_3-5-ratio1.500301
Spike_AFFX-r2-Bs-dap_M_signal260.038757
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.389753
Spike_AFFX-r2-Ec-bioB_avg-signal36.213409
Spike_AFFX-r2-Bs-thr_avg-signal85.995354
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal324.862610
Spike_AFFX-r2-Bs-phe_5_signal36.346672
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal502.559967
RawQ2.581122
Spike_AFFX-r2-Bs-lys_5_signal24.891727
Signal(A)3.560441
%A28.123631
Signal(All)130.550873
Corner+Avg:157,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal125.306396
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal63.907234
Spike_AFFX-r2-Ec-bioD_avg-signal413.711304
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.385796
Spike_AFFX-r2-Bs-lys_avg-signal31.574265
Spike_AFFX-r2-P1-cre_avg-signal2317.452881
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.490574
Spike_AFFX-r2-Bs-thr_3_signal125.027687
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.227947
Spike_AFFX-r2-Bs-dap_3_signal369.646240
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.546992
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal109.392250
#M340
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.345081
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.145478
Spike_AFFX-r2-Bs-thr_M_signal96.074348
Signal(P)183.775574
Spike_AFFX-r2-Bs-phe_3-5-ratio1.758269
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7371,Count:9
Spike_AFFX-r2-P1-cre_5_signal1806.537476
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6415
Signal(M)13.260238
BackgroundAvg:63.87,Std:0.53,Min:62.5,Max:65.7
Spike_AFFX-r2-Ec-bioC_avg-signal117.349319
Spike_AFFX-r2-Bs-dap_avg-signal253.974686
Spike_AFFX-r2-Bs-dap_3-5-ratio2.795287
Spike_AFFX-r2-Ec-bioB_5_signal39.097580
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.521266
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-7_Col0-1-18h_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_598-7_Col0-1-18h_Rep1_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-7_Col0-1-18h_Rep1_ATH1
Organism:
Stock Code:
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:0.494983
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-ratio1.236962
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.569043
Spike_AFFX-r2-Bs-dap_5_signal107.885017
NoiseAvg:3.21,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_signal37.921486
#P15900
Spike_AFFX-r2-Bs-phe_M_signal36.349380
Corner-Avg:9022,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal39.137005
Spike_AFFX-r2-Ec-bioB_3_signal23.803818
Spike_AFFX-r2-Bs-lys_M_signal15.359569
Spike_AFFX-r2-P1-cre_3_signal2032.542725
Spike_AFFX-r2-Bs-lys_3-5-ratio2.096406
Spike_AFFX-r2-Bs-dap_M_signal223.568054
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.732474
Spike_AFFX-r2-Ec-bioB_avg-signal34.924042
Spike_AFFX-r2-Bs-thr_avg-signal101.785858
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal289.013580
Spike_AFFX-r2-Bs-phe_5_signal58.327301
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal428.568054
RawQ2.889222
Spike_AFFX-r2-Bs-lys_5_signal27.012409
Signal(A)4.119396
%A28.645330
Signal(All)130.788391
Corner+Avg:154,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal87.327736
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.908222
Spike_AFFX-r2-Ec-bioD_avg-signal358.790833
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.706268
Spike_AFFX-r2-Bs-lys_avg-signal33.000320
Spike_AFFX-r2-P1-cre_avg-signal1837.858154
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.648400
Spike_AFFX-r2-Bs-thr_3_signal179.462463
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal49.194965
Spike_AFFX-r2-Bs-dap_3_signal360.491669
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.482865
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal82.219582
#M376
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.628983
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.062128
Spike_AFFX-r2-Bs-thr_M_signal87.973625
Signal(P)185.588867
Spike_AFFX-r2-Bs-phe_3-5-ratio0.907092
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6753,Count:9
Spike_AFFX-r2-P1-cre_5_signal1643.173462
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6534
Signal(M)14.638374
BackgroundAvg:66.40,Std:0.66,Min:64.6,Max:68.3
Spike_AFFX-r2-Ec-bioC_avg-signal84.773659
Spike_AFFX-r2-Bs-dap_avg-signal230.648239
Spike_AFFX-r2-Bs-dap_3-5-ratio3.341443
Spike_AFFX-r2-Ec-bioB_5_signal41.831299
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.494983
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-8_Col0-1-18h_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_598-8_Col0-1-18h_Rep2_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-8_Col0-1-18h_Rep2_ATH1
Organism:
Stock Code:
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:0.627685
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-ratio1.173073
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.712052
Spike_AFFX-r2-Bs-dap_5_signal279.964142
NoiseAvg:2.65,Std:0.11,Min:2.4,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal97.224274
#P15906
Spike_AFFX-r2-Bs-phe_M_signal84.229202
Corner-Avg:7561,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal62.950859
Spike_AFFX-r2-Ec-bioB_3_signal38.464230
Spike_AFFX-r2-Bs-lys_M_signal48.304546
Spike_AFFX-r2-P1-cre_3_signal2740.346436
Spike_AFFX-r2-Bs-lys_3-5-ratio1.844714
Spike_AFFX-r2-Bs-dap_M_signal517.574768
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.722390
Spike_AFFX-r2-Ec-bioB_avg-signal51.811306
Spike_AFFX-r2-Bs-thr_avg-signal229.378662
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal428.160126
Spike_AFFX-r2-Bs-phe_5_signal132.301743
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal554.179871
RawQ2.500369
Spike_AFFX-r2-Bs-lys_5_signal68.389320
Signal(A)4.004663
%A28.658484
Signal(All)131.044937
Corner+Avg:131,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal137.554108
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal91.196320
Spike_AFFX-r2-Ec-bioD_avg-signal491.169983
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.732574
Spike_AFFX-r2-Bs-lys_avg-signal80.950867
Spike_AFFX-r2-P1-cre_avg-signal2538.193359
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal361.906677
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-signal102.575752
Spike_AFFX-r2-Bs-dap_3_signal852.847168
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.294329
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal121.474510
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal126.158737
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.132370
Spike_AFFX-r2-Bs-thr_M_signal229.005066
Signal(P)185.938736
Spike_AFFX-r2-Bs-phe_3-5-ratio0.689305
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6119,Count:9
Spike_AFFX-r2-P1-cre_5_signal2336.040039
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6537
Signal(M)14.754730
BackgroundAvg:58.47,Std:0.94,Min:55.7,Max:61.2
Spike_AFFX-r2-Ec-bioC_avg-signal129.514313
Spike_AFFX-r2-Bs-dap_avg-signal550.128662
Spike_AFFX-r2-Bs-dap_3-5-ratio3.046273
Spike_AFFX-r2-Ec-bioB_5_signal54.018829
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.627685
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-9_Col0-1-18h_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_598-9_Col0-1-18h_Rep3_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-9_Col0-1-18h_Rep3_ATH1
Organism:
Stock Code:
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:0.511699
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-ratio1.397779
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.921857
Spike_AFFX-r2-Bs-dap_5_signal125.142181
NoiseAvg:2.67,Std:0.09,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal41.996346
#P16159
Spike_AFFX-r2-Bs-phe_M_signal34.451931
Corner-Avg:7156,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal44.404907
Spike_AFFX-r2-Ec-bioB_3_signal33.745762
Spike_AFFX-r2-Bs-lys_M_signal18.657688
Spike_AFFX-r2-P1-cre_3_signal2429.558594
Spike_AFFX-r2-Bs-lys_3-5-ratio1.930607
Spike_AFFX-r2-Bs-dap_M_signal227.431000
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.822111
Spike_AFFX-r2-Ec-bioB_avg-signal38.252316
Spike_AFFX-r2-Bs-thr_avg-signal101.772453
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal339.925140
Spike_AFFX-r2-Bs-phe_5_signal45.867718
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal429.208374
RawQ2.525830
Spike_AFFX-r2-Bs-lys_5_signal26.259975
Signal(A)3.392546
%A27.536169
Signal(All)129.981873
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal128.492249
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal56.503960
Spike_AFFX-r2-Ec-bioD_avg-signal384.566772
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.841736
Spike_AFFX-r2-Bs-lys_avg-signal31.871780
Spike_AFFX-r2-P1-cre_avg-signal2083.857422
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.622096
Spike_AFFX-r2-Bs-thr_3_signal160.514679
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-signal45.607868
Spike_AFFX-r2-Bs-dap_3_signal350.884766
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.262656
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal114.311768
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.697681
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.124051
Spike_AFFX-r2-Bs-thr_M_signal102.806343
Signal(P)181.871201
Spike_AFFX-r2-Bs-phe_3-5-ratio1.231889
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6526,Count:9
Spike_AFFX-r2-P1-cre_5_signal1738.156494
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6281
Signal(M)12.759646
BackgroundAvg:58.16,Std:0.57,Min:56.7,Max:59.8
Spike_AFFX-r2-Ec-bioC_avg-signal121.402008
Spike_AFFX-r2-Bs-dap_avg-signal234.486008
Spike_AFFX-r2-Bs-dap_3-5-ratio2.803889
Spike_AFFX-r2-Ec-bioB_5_signal36.606281
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.511699
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-10_513-13-Control_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_598-10_513-13-Control_Rep1_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-10_513-13-Control_Rep1_ATH1
Organism:
Stock Code:
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:0.436715
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-ratio1.319672
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.831662
Spike_AFFX-r2-Bs-dap_5_signal142.335434
NoiseAvg:2.57,Std:0.06,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal47.696671
#P16290
Spike_AFFX-r2-Bs-phe_M_signal43.628773
Corner-Avg:8093,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal51.208702
Spike_AFFX-r2-Ec-bioB_3_signal34.168938
Spike_AFFX-r2-Bs-lys_M_signal21.890137
Spike_AFFX-r2-P1-cre_3_signal2335.001221
Spike_AFFX-r2-Bs-lys_3-5-ratio1.780235
Spike_AFFX-r2-Bs-dap_M_signal262.589661
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.875015
Spike_AFFX-r2-Ec-bioB_avg-signal42.154251
Spike_AFFX-r2-Bs-thr_avg-signal111.642906
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal372.288208
Spike_AFFX-r2-Bs-phe_5_signal63.374470
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal544.625732
RawQ2.418025
Spike_AFFX-r2-Bs-lys_5_signal31.555380
Signal(A)2.808323
%A27.246822
Signal(All)132.075348
Corner+Avg:126,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal123.943054
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.172997
Spike_AFFX-r2-Ec-bioD_avg-signal458.456970
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.416046
Spike_AFFX-r2-Bs-lys_avg-signal36.540501
Spike_AFFX-r2-P1-cre_avg-signal2052.190918
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.337133
Spike_AFFX-r2-Bs-thr_3_signal184.825287
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal56.058746
Spike_AFFX-r2-Bs-dap_3_signal408.814911
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.462914
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal111.416527
#M305
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.175980
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.112430
Spike_AFFX-r2-Bs-thr_M_signal102.406776
Signal(P)183.659119
Spike_AFFX-r2-Bs-phe_3-5-ratio0.965262
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7266,Count:9
Spike_AFFX-r2-P1-cre_5_signal1769.380493
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6215
Signal(M)11.075625
BackgroundAvg:56.24,Std:0.28,Min:55.3,Max:57.1
Spike_AFFX-r2-Ec-bioC_avg-signal117.679794
Spike_AFFX-r2-Bs-dap_avg-signal271.246674
Spike_AFFX-r2-Bs-dap_3-5-ratio2.872194
Spike_AFFX-r2-Ec-bioB_5_signal41.085110
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.436715
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-11_513-13-Control_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_598-11_513-13-Control_Rep2_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-11_513-13-Control_Rep2_ATH1
Organism:
Stock Code:
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:0.477967
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-ratio1.304559
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.174390
Spike_AFFX-r2-Bs-dap_5_signal267.003357
NoiseAvg:2.91,Std:0.14,Min:2.5,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_signal99.543152
#P16224
Spike_AFFX-r2-Bs-phe_M_signal87.658257
Corner-Avg:8701,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal53.219345
Spike_AFFX-r2-Ec-bioB_3_signal42.452023
Spike_AFFX-r2-Bs-lys_M_signal50.317863
Spike_AFFX-r2-P1-cre_3_signal2504.128174
Spike_AFFX-r2-Bs-lys_3-5-ratio1.397660
Spike_AFFX-r2-Bs-dap_M_signal513.726379
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.962928
Spike_AFFX-r2-Ec-bioB_avg-signal43.939835
Spike_AFFX-r2-Bs-thr_avg-signal236.247437
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal399.489258
Spike_AFFX-r2-Bs-phe_5_signal131.681351
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal586.981628
RawQ2.691930
Spike_AFFX-r2-Bs-lys_5_signal73.937386
Signal(A)3.027508
%A27.544937
Signal(All)131.290115
Corner+Avg:147,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal147.313599
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal129.229401
Spike_AFFX-r2-Ec-bioD_avg-signal493.235443
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.126701
Spike_AFFX-r2-Bs-lys_avg-signal75.864868
Spike_AFFX-r2-P1-cre_avg-signal2211.824707
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.328365
Spike_AFFX-r2-Bs-thr_3_signal394.482330
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-signal116.189674
Spike_AFFX-r2-Bs-dap_3_signal858.911621
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.469330
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal141.133911
#M303
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal103.339348
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.043786
Spike_AFFX-r2-Bs-thr_M_signal214.716827
Signal(P)183.191528
Spike_AFFX-r2-Bs-phe_3-5-ratio0.981380
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7708,Count:9
Spike_AFFX-r2-P1-cre_5_signal1919.520996
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6283
Signal(M)11.901921
BackgroundAvg:64.58,Std:1.23,Min:62.1,Max:68.6
Spike_AFFX-r2-Ec-bioC_avg-signal144.223755
Spike_AFFX-r2-Bs-dap_avg-signal546.547119
Spike_AFFX-r2-Bs-dap_3-5-ratio3.216857
Spike_AFFX-r2-Ec-bioB_5_signal36.148132
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.477967
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-12_513-13-Control_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_598-12_513-13-Control_Rep3_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-12_513-13-Control_Rep3_ATH1
Organism:
Stock Code:
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:0.452289
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-ratio1.360298
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.919452
Spike_AFFX-r2-Bs-dap_5_signal93.223465
NoiseAvg:2.95,Std:0.10,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal42.045807
#P16012
Spike_AFFX-r2-Bs-phe_M_signal33.309803
Corner-Avg:7433,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal41.756954
Spike_AFFX-r2-Ec-bioB_3_signal26.378380
Spike_AFFX-r2-Bs-lys_M_signal17.752363
Spike_AFFX-r2-P1-cre_3_signal1907.377075
Spike_AFFX-r2-Bs-lys_3-5-ratio1.238807
Spike_AFFX-r2-Bs-dap_M_signal197.600540
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.947890
Spike_AFFX-r2-Ec-bioB_avg-signal32.274860
Spike_AFFX-r2-Bs-thr_avg-signal64.487747
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal241.280899
Spike_AFFX-r2-Bs-phe_5_signal44.457970
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal403.154144
RawQ2.658255
Spike_AFFX-r2-Bs-lys_5_signal24.272877
Signal(A)3.411450
%A28.189390
Signal(All)131.516708
Corner+Avg:113,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal107.315262
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.807129
Spike_AFFX-r2-Ec-bioD_avg-signal322.217529
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.197281
Spike_AFFX-r2-Bs-lys_avg-signal24.031553
Spike_AFFX-r2-P1-cre_avg-signal1654.776367
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.613328
Spike_AFFX-r2-Bs-thr_3_signal81.900604
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal40.858299
Spike_AFFX-r2-Bs-dap_3_signal262.036133
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.670891
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal79.745934
#M368
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.069418
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.345715
Spike_AFFX-r2-Bs-thr_M_signal69.516830
Signal(P)185.701263
Spike_AFFX-r2-Bs-phe_3-5-ratio1.007854
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7816,Count:9
Spike_AFFX-r2-P1-cre_5_signal1402.175659
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6430
Signal(M)12.259752
BackgroundAvg:65.06,Std:0.99,Min:62.3,Max:67.2
Spike_AFFX-r2-Ec-bioC_avg-signal93.530594
Spike_AFFX-r2-Bs-dap_avg-signal184.286697
Spike_AFFX-r2-Bs-dap_3-5-ratio2.810839
Spike_AFFX-r2-Ec-bioB_5_signal28.689251
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.452289
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-13_513-13-6h_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_598-13_513-13-6h_Rep1_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-13_513-13-6h_Rep1_ATH1
Organism:
Stock Code:
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:0.365632
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-ratio1.053690
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.117724
Spike_AFFX-r2-Bs-dap_5_signal98.725990
NoiseAvg:2.92,Std:0.11,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal37.459347
#P16254
Spike_AFFX-r2-Bs-phe_M_signal34.695812
Corner-Avg:12688,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal69.527649
Spike_AFFX-r2-Ec-bioB_3_signal61.031158
Spike_AFFX-r2-Bs-lys_M_signal13.348241
Spike_AFFX-r2-P1-cre_3_signal2375.851563
Spike_AFFX-r2-Bs-lys_3-5-ratio2.371555
Spike_AFFX-r2-Bs-dap_M_signal219.293259
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.217747
Spike_AFFX-r2-Ec-bioB_avg-signal61.720623
Spike_AFFX-r2-Bs-thr_avg-signal84.213646
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal479.246918
Spike_AFFX-r2-Bs-phe_5_signal45.470840
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal757.361816
RawQ2.568245
Spike_AFFX-r2-Bs-lys_5_signal27.587803
Signal(A)2.676305
%A27.400263
Signal(All)131.537323
Corner+Avg:205,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal191.387802
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal49.011238
Spike_AFFX-r2-Ec-bioD_avg-signal618.304382
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.258217
Spike_AFFX-r2-Bs-lys_avg-signal35.454014
Spike_AFFX-r2-P1-cre_avg-signal2315.322266
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.341517
Spike_AFFX-r2-Bs-thr_3_signal120.534706
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-signal43.059296
Spike_AFFX-r2-Bs-dap_3_signal298.489655
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.580317
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal185.691574
#M306
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal65.425995
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.030676
Spike_AFFX-r2-Bs-thr_M_signal94.646881
Signal(P)183.346634
Spike_AFFX-r2-Bs-phe_3-5-ratio1.077861
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9804,Count:9
Spike_AFFX-r2-P1-cre_5_signal2254.792725
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6250
Signal(M)11.513193
BackgroundAvg:58.57,Std:0.87,Min:56.8,Max:60.7
Spike_AFFX-r2-Ec-bioC_avg-signal188.539688
Spike_AFFX-r2-Bs-dap_avg-signal205.502975
Spike_AFFX-r2-Bs-dap_3-5-ratio3.023415
Spike_AFFX-r2-Ec-bioB_5_signal54.603050
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.365632
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-14_513-13-6h_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_598-14_513-13-6h_Rep2_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-14_513-13-6h_Rep2_ATH1
Organism:
Stock Code:
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:0.412411
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-ratio1.190425
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.836205
Spike_AFFX-r2-Bs-dap_5_signal54.428715
NoiseAvg:2.69,Std:0.11,Min:2.4,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_signal29.742083
#P16350
Spike_AFFX-r2-Bs-phe_M_signal18.065727
Corner-Avg:12628,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal94.680031
Spike_AFFX-r2-Ec-bioB_3_signal56.511627
Spike_AFFX-r2-Bs-lys_M_signal8.604226
Spike_AFFX-r2-P1-cre_3_signal2741.668701
Spike_AFFX-r2-Bs-lys_3-5-ratio1.938302
Spike_AFFX-r2-Bs-dap_M_signal165.402039
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.676487
Spike_AFFX-r2-Ec-bioB_avg-signal72.924232
Spike_AFFX-r2-Bs-thr_avg-signal56.718441
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal515.019104
Spike_AFFX-r2-Bs-phe_5_signal37.448040
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal843.445557
RawQ2.602767
Spike_AFFX-r2-Bs-lys_5_signal22.738131
Signal(A)2.609564
%A27.032003
Signal(All)132.669708
Corner+Avg:199,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal251.612320
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.000278
Spike_AFFX-r2-Ec-bioD_avg-signal679.232300
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.679085
Spike_AFFX-r2-Bs-lys_avg-signal25.138573
Spike_AFFX-r2-P1-cre_avg-signal2522.384277
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.288908
Spike_AFFX-r2-Bs-thr_3_signal79.604286
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.504683
Spike_AFFX-r2-Bs-dap_3_signal209.242523
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.637698
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.221481
#M294
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.073364
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.163679
Spike_AFFX-r2-Bs-thr_M_signal60.808945
Signal(P)183.904007
Spike_AFFX-r2-Bs-phe_3-5-ratio1.041451
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9979,Count:9
Spike_AFFX-r2-P1-cre_5_signal2303.100098
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6166
Signal(M)11.139218
BackgroundAvg:59.86,Std:0.56,Min:58.7,Max:61.8
Spike_AFFX-r2-Ec-bioC_avg-signal233.916901
Spike_AFFX-r2-Bs-dap_avg-signal143.024429
Spike_AFFX-r2-Bs-dap_3-5-ratio3.844341
Spike_AFFX-r2-Ec-bioB_5_signal67.581047
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.412411
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-15_513-13-6h_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_598-15_513-13-6h_Rep3_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-15_513-13-6h_Rep3_ATH1
Organism:
Stock Code:
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:0.373203
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-ratio1.223283
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.835469
Spike_AFFX-r2-Bs-dap_5_signal70.564888
NoiseAvg:2.74,Std:0.08,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal37.416916
#P16442
Spike_AFFX-r2-Bs-phe_M_signal36.101185
Corner-Avg:12763,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.590240
Spike_AFFX-r2-Ec-bioB_3_signal53.371967
Spike_AFFX-r2-Bs-lys_M_signal20.167273
Spike_AFFX-r2-P1-cre_3_signal2752.120850
Spike_AFFX-r2-Bs-lys_3-5-ratio2.529578
Spike_AFFX-r2-Bs-dap_M_signal186.203384
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.316310
Spike_AFFX-r2-Ec-bioB_avg-signal65.948280
Spike_AFFX-r2-Bs-thr_avg-signal82.571281
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal555.975220
Spike_AFFX-r2-Bs-phe_5_signal51.357059
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal828.860657
RawQ2.590335
Spike_AFFX-r2-Bs-lys_5_signal25.745003
Signal(A)2.356379
%A26.611135
Signal(All)132.824921
Corner+Avg:208,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal208.791153
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.869690
Spike_AFFX-r2-Ec-bioD_avg-signal692.417969
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P72.082420
Spike_AFFX-r2-Bs-lys_avg-signal37.012089
Spike_AFFX-r2-P1-cre_avg-signal2500.951660
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.306445
Spike_AFFX-r2-Bs-thr_3_signal124.086090
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-signal46.109310
Spike_AFFX-r2-Bs-dap_3_signal249.931610
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.490823
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal213.544250
#M298
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal65.123993
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.977742
Spike_AFFX-r2-Bs-thr_M_signal86.210846
Signal(P)183.209503
Spike_AFFX-r2-Bs-phe_3-5-ratio0.990510
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9668,Count:9
Spike_AFFX-r2-P1-cre_5_signal2249.782471
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6070
Signal(M)10.410542
BackgroundAvg:62.75,Std:0.59,Min:61.3,Max:65.0
Spike_AFFX-r2-Ec-bioC_avg-signal211.167694
Spike_AFFX-r2-Bs-dap_avg-signal168.899963
Spike_AFFX-r2-Bs-dap_3-5-ratio3.541869
Spike_AFFX-r2-Ec-bioB_5_signal63.882637
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.373203
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-16_513-13-18h_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_598-16_513-13-18h_Rep1_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-16_513-13-18h_Rep1_ATH1
Organism:
Stock Code:
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:0.314053
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-ratio1.159212
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.119895
Spike_AFFX-r2-Bs-dap_5_signal101.813148
NoiseAvg:2.90,Std:0.11,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal36.500515
#P16574
Spike_AFFX-r2-Bs-phe_M_signal35.234406
Corner-Avg:15137,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal73.090599
Spike_AFFX-r2-Ec-bioB_3_signal60.380993
Spike_AFFX-r2-Bs-lys_M_signal16.529537
Spike_AFFX-r2-P1-cre_3_signal2197.773438
Spike_AFFX-r2-Bs-lys_3-5-ratio1.831079
Spike_AFFX-r2-Bs-dap_M_signal217.331467
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.602095
Spike_AFFX-r2-Ec-bioB_avg-signal62.462753
Spike_AFFX-r2-Bs-thr_avg-signal73.456352
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal404.420166
Spike_AFFX-r2-Bs-phe_5_signal47.479656
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal672.911072
RawQ2.623991
Spike_AFFX-r2-Bs-lys_5_signal26.462135
Signal(A)2.229040
%A26.093819
Signal(All)130.841400
Corner+Avg:298,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal188.824982
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal45.249352
Spike_AFFX-r2-Ec-bioD_avg-signal538.665649
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P72.661110
Spike_AFFX-r2-Bs-lys_avg-signal30.481977
Spike_AFFX-r2-P1-cre_avg-signal2046.846924
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.245068
Spike_AFFX-r2-Bs-thr_3_signal94.977798
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal42.654469
Spike_AFFX-r2-Bs-dap_3_signal276.085083
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.663891
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal155.867691
#M284
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.454262
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.211444
Spike_AFFX-r2-Bs-thr_M_signal88.890739
Signal(P)179.095596
Spike_AFFX-r2-Bs-phe_3-5-ratio0.953026
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11416,Count:9
Spike_AFFX-r2-P1-cre_5_signal1895.920410
Spike_AFFX-r2-Bs-phe_M_detectionP
#A5952
Signal(M)10.192087
BackgroundAvg:63.59,Std:0.84,Min:61.4,Max:65.8
Spike_AFFX-r2-Ec-bioC_avg-signal172.346344
Spike_AFFX-r2-Bs-dap_avg-signal198.409912
Spike_AFFX-r2-Bs-dap_3-5-ratio2.711684
Spike_AFFX-r2-Ec-bioB_5_signal53.916676
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.314053
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-17_513-13-18h_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_598-17_513-13-18h_Rep2_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-17_513-13-18h_Rep2_ATH1
Organism:
Stock Code:
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:0.355795
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-ratio1.104655
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.781642
Spike_AFFX-r2-Bs-dap_5_signal96.154648
NoiseAvg:3.22,Std:0.37,Min:2.7,Max:5.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.033283
#P16333
Spike_AFFX-r2-Bs-phe_M_signal23.407104
Corner-Avg:12964,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.071503
Spike_AFFX-r2-Ec-bioB_3_signal47.500633
Spike_AFFX-r2-Bs-lys_M_signal11.972578
Spike_AFFX-r2-P1-cre_3_signal2475.422607
Spike_AFFX-r2-Bs-lys_3-5-ratio2.349431
Spike_AFFX-r2-Bs-dap_M_signal169.742752
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.655948
Spike_AFFX-r2-Ec-bioB_avg-signal58.114151
Spike_AFFX-r2-Bs-thr_avg-signal61.830215
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal427.964142
Spike_AFFX-r2-Bs-phe_5_signal42.984913
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal637.606812
RawQ2.678519
Spike_AFFX-r2-Bs-lys_5_signal24.556175
Signal(A)2.717331
%A26.896099
Signal(All)132.384323
Corner+Avg:208,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal173.906830
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.860569
Spike_AFFX-r2-Ec-bioD_avg-signal532.785461
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.604561
Spike_AFFX-r2-Bs-lys_avg-signal31.407265
Spike_AFFX-r2-P1-cre_avg-signal2358.162109
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.499342
Spike_AFFX-r2-Bs-thr_3_signal82.422783
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal36.084194
Spike_AFFX-r2-Bs-dap_3_signal268.241608
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.489860
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal165.182999
#M342
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.693039
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.052813
Spike_AFFX-r2-Bs-thr_M_signal72.034584
Signal(P)183.621216
Spike_AFFX-r2-Bs-phe_3-5-ratio0.973843
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9673,Count:9
Spike_AFFX-r2-P1-cre_5_signal2240.901367
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6135
Signal(M)11.492655
BackgroundAvg:63.70,Std:1.02,Min:60.4,Max:66.0
Spike_AFFX-r2-Ec-bioC_avg-signal169.544922
Spike_AFFX-r2-Bs-dap_avg-signal178.046341
Spike_AFFX-r2-Bs-dap_3-5-ratio2.789690
Spike_AFFX-r2-Ec-bioB_5_signal60.770321
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.355795
NF1.000000
HZ4
Tau0.015000

Slide: Khan_598-18_513-13-18h_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_598-18_513-13-18h_Rep3_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Khan_598-18_513-13-18h_Rep3_ATH1
Organism:
Stock Code:
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:0.405796
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-ratio1.069369
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.890346
Spike_AFFX-r2-Bs-dap_5_signal82.106232
NoiseAvg:2.92,Std:0.15,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal35.880753
#P16295
Spike_AFFX-r2-Bs-phe_M_signal18.449108
Corner-Avg:11459,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal65.779099
Spike_AFFX-r2-Ec-bioB_3_signal48.454247
Spike_AFFX-r2-Bs-lys_M_signal13.002502
Spike_AFFX-r2-P1-cre_3_signal2407.038086
Spike_AFFX-r2-Bs-lys_3-5-ratio2.263032
Spike_AFFX-r2-Bs-dap_M_signal196.843643
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.150017
Spike_AFFX-r2-Ec-bioB_avg-signal56.218395
Spike_AFFX-r2-Bs-thr_avg-signal60.350506
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal413.819336
Spike_AFFX-r2-Bs-phe_5_signal35.505096
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal722.116821
RawQ2.695856
Spike_AFFX-r2-Bs-lys_5_signal21.321943
Signal(A)2.784271
%A27.216133
Signal(All)132.835449
Corner+Avg:176,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal187.925949
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.649649
Spike_AFFX-r2-Ec-bioD_avg-signal567.968079
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.437965
Spike_AFFX-r2-Bs-lys_avg-signal27.525560
Spike_AFFX-r2-P1-cre_avg-signal2328.966797
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_signal77.144211
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.534616
Spike_AFFX-r2-Bs-dap_3_signal233.475433
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.745005
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.835037
#M307
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.252239
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.033497
Spike_AFFX-r2-Bs-thr_M_signal68.026550
Signal(P)184.680206
Spike_AFFX-r2-Bs-phe_3-5-ratio0.806917
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9748,Count:9
Spike_AFFX-r2-P1-cre_5_signal2250.895508
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6208
Signal(M)10.839597
BackgroundAvg:66.41,Std:0.58,Min:64.9,Max:68.0
Spike_AFFX-r2-Ec-bioC_avg-signal184.880493
Spike_AFFX-r2-Bs-dap_avg-signal170.808426
Spike_AFFX-r2-Bs-dap_3-5-ratio2.843577
Spike_AFFX-r2-Ec-bioB_5_signal54.421837
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.405796
NF1.000000
HZ4
Tau0.015000


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