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Experiment: Transcriptome comparison of a lignin-deficient mutant and the wildtype

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-621

Gb is a novel lignin deficient mutant with reduced lignification in inflorescence stem. The objective of this transcript profiling analysis is to study the potential transcriptome difference between this Gb mutant and the wildtype.

About the Experimenter

Name:Dr Yuguo Xiao
Head of Lab Name:Prof Claire Halpin
Lab:
Address:Division of Plant Sciences, College of Life Sciences, University of Dundee account (DEL0), Scottish Crop Research Institute (SCRI)
Errol Road, Invergowrie, Dundee, Tayside Region, DD2 5DA, UNITED KINGDOM
Postcode: DD2 5DA
Country: UNITED KINGDOM
 

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_out
Number of Slides:8
 
Experimental Parameters:
parametergene_knock_in
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Xiao: Transcriptome comparison of a lignin-deficient mutant and the wildtype

Slide: Xiao_621-1_Col-0_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Xiao_621-1_Col-0_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-1_Col-0_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4-week-old
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:0.385519
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-ratio1.349517
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.599918
Spike_AFFX-r2-Bs-dap_5_signal39.017960
NoiseAvg:3.43,Std:0.09,Min:3.1,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal7.398405
#P14404
Spike_AFFX-r2-Bs-phe_M_signal29.595329
Corner-Avg:12598,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal11.598081
Spike_AFFX-r2-Ec-bioB_3_signal7.294991
Spike_AFFX-r2-Bs-lys_M_signal19.005491
Spike_AFFX-r2-P1-cre_3_signal3205.545166
Spike_AFFX-r2-Bs-lys_3-5-ratio2.784520
Spike_AFFX-r2-Bs-dap_M_signal134.634567
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.826915
Spike_AFFX-r2-Ec-bioB_avg-signal10.351017
Spike_AFFX-r2-Bs-thr_avg-signal52.862133
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal683.520569
Spike_AFFX-r2-Bs-phe_5_signal21.958889
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal942.908081
RawQ2.657629
Spike_AFFX-r2-Bs-lys_5_signal22.546700
Signal(A)3.634741
%A35.278385
Signal(All)136.431137
Corner+Avg:261,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal155.838333
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal51.145271
Spike_AFFX-r2-Ec-bioD_avg-signal813.214355
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.147743
Spike_AFFX-r2-Bs-lys_avg-signal34.777981
Spike_AFFX-r2-P1-cre_avg-signal2790.436035
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.573871
Spike_AFFX-r2-Bs-thr_3_signal117.093918
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal34.233166
Spike_AFFX-r2-Bs-dap_3_signal337.815460
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.379488
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal137.948303
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal62.781746
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.129686
Spike_AFFX-r2-Bs-thr_M_signal34.094074
Signal(P)213.667206
Spike_AFFX-r2-Bs-phe_3-5-ratio2.329138
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11351,Count:9
Spike_AFFX-r2-P1-cre_5_signal2375.327148
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8047
Signal(M)14.158918
BackgroundAvg:62.71,Std:0.39,Min:60.9,Max:63.8
Spike_AFFX-r2-Ec-bioC_avg-signal146.893311
Spike_AFFX-r2-Bs-dap_avg-signal170.489319
Spike_AFFX-r2-Bs-dap_3-5-ratio8.657948
Spike_AFFX-r2-Ec-bioB_5_signal12.159982
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.385519
NF1.000000
HZ4
Tau0.015000

Slide: Xiao_621-2_Col-0_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 ("Xiao_621-2_Col-0_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-2_Col-0_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4-week-old
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:0.42222
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-ratio1.349717
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.542945
Spike_AFFX-r2-Bs-dap_5_signal38.990997
NoiseAvg:3.15,Std:0.10,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.648934
#P14373
Spike_AFFX-r2-Bs-phe_M_signal26.266195
Corner-Avg:12730,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.197491
Spike_AFFX-r2-Ec-bioB_3_signal7.545238
Spike_AFFX-r2-Bs-lys_M_signal20.009340
Spike_AFFX-r2-P1-cre_3_signal3754.424561
Spike_AFFX-r2-Bs-lys_3-5-ratio2.404397
Spike_AFFX-r2-Bs-dap_M_signal141.000610
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.566851
Spike_AFFX-r2-Ec-bioB_avg-signal10.546533
Spike_AFFX-r2-Bs-thr_avg-signal41.548344
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal730.995850
Spike_AFFX-r2-Bs-phe_5_signal33.025459
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal995.941345
RawQ2.634237
Spike_AFFX-r2-Bs-lys_5_signal21.632351
Signal(A)3.684715
%A35.414291
Signal(All)138.233353
Corner+Avg:217,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal174.299301
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal45.190613
Spike_AFFX-r2-Ec-bioD_avg-signal863.468628
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.011837
Spike_AFFX-r2-Bs-lys_avg-signal31.218149
Spike_AFFX-r2-P1-cre_avg-signal3268.031250
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.573871
Spike_AFFX-r2-Bs-thr_3_signal88.474075
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal34.827423
Spike_AFFX-r2-Bs-dap_3_signal383.945465
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.362445
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal165.290833
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal52.012756
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.054501
Spike_AFFX-r2-Bs-thr_M_signal28.522020
Signal(P)216.966980
Spike_AFFX-r2-Bs-phe_3-5-ratio1.368357
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11317,Count:9
Spike_AFFX-r2-P1-cre_5_signal2781.637695
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8078
Signal(M)13.568545
BackgroundAvg:61.94,Std:0.42,Min:61.1,Max:63.4
Spike_AFFX-r2-Ec-bioC_avg-signal169.795074
Spike_AFFX-r2-Bs-dap_avg-signal187.979004
Spike_AFFX-r2-Bs-dap_3-5-ratio9.847029
Spike_AFFX-r2-Ec-bioB_5_signal13.896868
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.422220
NF1.000000
HZ4
Tau0.015000

Slide: Xiao_621-3_Col-0_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 ("Xiao_621-3_Col-0_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-3_Col-0_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4-week-old
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:0.510049
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-ratio1.342589
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.024133
Spike_AFFX-r2-Bs-dap_5_signal33.942215
NoiseAvg:3.08,Std:0.08,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.202580
#P14077
Spike_AFFX-r2-Bs-phe_M_signal38.829449
Corner-Avg:12371,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal7.432649
Spike_AFFX-r2-Ec-bioB_3_signal8.702651
Spike_AFFX-r2-Bs-lys_M_signal19.417400
Spike_AFFX-r2-P1-cre_3_signal3823.532471
Spike_AFFX-r2-Bs-lys_3-5-ratio1.968069
Spike_AFFX-r2-Bs-dap_M_signal148.191544
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.475591
Spike_AFFX-r2-Ec-bioB_avg-signal8.210960
Spike_AFFX-r2-Bs-thr_avg-signal49.063660
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal700.511169
Spike_AFFX-r2-Bs-phe_5_signal27.850731
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1110.724243
RawQ2.737946
Spike_AFFX-r2-Bs-lys_5_signal21.625658
Signal(A)3.990346
%A36.650593
Signal(All)141.444443
Corner+Avg:212,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal164.863571
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal48.974171
Spike_AFFX-r2-Ec-bioD_avg-signal905.617676
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.714161
Spike_AFFX-r2-Bs-lys_avg-signal27.867945
Spike_AFFX-r2-P1-cre_avg-signal3335.705566
Spike_AFFX-r2-Ec-bioB_M_detectionM
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.635248
Spike_AFFX-r2-Bs-thr_3_signal104.261604
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-signal38.551449
Spike_AFFX-r2-Bs-dap_3_signal312.023804
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.585591
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.162415
#M373
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.560780
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.946608
Spike_AFFX-r2-Bs-thr_M_signal35.726803
Signal(P)226.417130
Spike_AFFX-r2-Bs-phe_3-5-ratio1.758452
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10624,Count:9
Spike_AFFX-r2-P1-cre_5_signal2847.878906
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8360
Signal(M)15.320295
BackgroundAvg:64.71,Std:0.57,Min:63.2,Max:66.0
Spike_AFFX-r2-Ec-bioC_avg-signal169.513000
Spike_AFFX-r2-Bs-dap_avg-signal164.719177
Spike_AFFX-r2-Bs-dap_3-5-ratio9.192795
Spike_AFFX-r2-Ec-bioB_5_signal8.497581
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.510049
NF1.000000
HZ4
Tau0.015000

Slide: Xiao_621-4_Col-0_Rep4_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 ("Xiao_621-4_Col-0_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-4_Col-0_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4-week-old
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:0.50929
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-ratio1.308864
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.869042
Spike_AFFX-r2-Bs-dap_5_signal37.770969
NoiseAvg:2.97,Std:0.10,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.074398
#P14130
Spike_AFFX-r2-Bs-phe_M_signal20.687168
Corner-Avg:12057,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal16.240038
Spike_AFFX-r2-Ec-bioB_3_signal11.566420
Spike_AFFX-r2-Bs-lys_M_signal16.961147
Spike_AFFX-r2-P1-cre_3_signal3950.682129
Spike_AFFX-r2-Bs-lys_3-5-ratio3.569140
Spike_AFFX-r2-Bs-dap_M_signal140.289551
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.923569
Spike_AFFX-r2-Ec-bioB_avg-signal13.705284
Spike_AFFX-r2-Bs-thr_avg-signal35.718235
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal871.842041
Spike_AFFX-r2-Bs-phe_5_signal22.693853
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1047.913452
RawQ2.535739
Spike_AFFX-r2-Bs-lys_5_signal15.923773
Signal(A)3.961855
%A36.444542
Signal(All)140.637634
Corner+Avg:223,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal175.760818
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.766136
Spike_AFFX-r2-Ec-bioD_avg-signal959.877747
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.946514
Spike_AFFX-r2-Bs-lys_avg-signal29.906364
Spike_AFFX-r2-P1-cre_avg-signal3484.543945
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_signal70.203278
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.715719
Spike_AFFX-r2-Bs-dap_3_signal331.078278
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.201953
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal162.985626
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.834175
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.078382
Spike_AFFX-r2-Bs-thr_M_signal29.877029
Signal(P)224.311539
Spike_AFFX-r2-Bs-phe_3-5-ratio1.487898
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10594,Count:9
Spike_AFFX-r2-P1-cre_5_signal3018.405518
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8313
Signal(M)14.952611
BackgroundAvg:61.15,Std:0.67,Min:59.0,Max:63.0
Spike_AFFX-r2-Ec-bioC_avg-signal169.373230
Spike_AFFX-r2-Bs-dap_avg-signal169.712936
Spike_AFFX-r2-Bs-dap_3-5-ratio8.765416
Spike_AFFX-r2-Ec-bioB_5_signal13.309397
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.509290
NF1.000000
HZ4
Tau0.015000

Slide: Xiao_621-5_Gb-mutant _Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Xiao_621-5_Gb-mutant _Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-5_Gb-mutant _Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_023077 (AZ)
Stock Code:
Age: 4-week-old
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:0.457766
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-ratio1.302399
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.033856
Spike_AFFX-r2-Bs-dap_5_signal25.218334
NoiseAvg:3.13,Std:0.07,Min:3.0,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_signal6.851121
#P14217
Spike_AFFX-r2-Bs-phe_M_signal26.050547
Corner-Avg:12038,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.426841
Spike_AFFX-r2-Ec-bioB_3_signal11.529368
Spike_AFFX-r2-Bs-lys_M_signal19.153032
Spike_AFFX-r2-P1-cre_3_signal3690.617432
Spike_AFFX-r2-Bs-lys_3-5-ratio2.538270
Spike_AFFX-r2-Bs-dap_M_signal124.540817
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.276147
Spike_AFFX-r2-Ec-bioB_avg-signal11.036008
Spike_AFFX-r2-Bs-thr_avg-signal45.795353
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal747.038147
Spike_AFFX-r2-Bs-phe_5_signal21.420996
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal907.952576
RawQ2.502414
Spike_AFFX-r2-Bs-lys_5_signal18.838335
Signal(A)3.881712
%A36.071899
Signal(All)138.910080
Corner+Avg:213,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal155.497879
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.877403
Spike_AFFX-r2-Ec-bioD_avg-signal827.495361
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.327927
Spike_AFFX-r2-Bs-lys_avg-signal28.602713
Spike_AFFX-r2-P1-cre_avg-signal3262.162598
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal104.658737
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-signal31.449648
Spike_AFFX-r2-Bs-dap_3_signal329.499359
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.215403
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal152.561615
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.816772
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.019246
Spike_AFFX-r2-Bs-thr_M_signal25.876200
Signal(P)220.238739
Spike_AFFX-r2-Bs-phe_3-5-ratio2.188386
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10329,Count:9
Spike_AFFX-r2-P1-cre_5_signal2833.707764
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8228
Signal(M)14.975125
BackgroundAvg:62.04,Std:0.57,Min:60.6,Max:64.0
Spike_AFFX-r2-Ec-bioC_avg-signal154.029755
Spike_AFFX-r2-Bs-dap_avg-signal159.752823
Spike_AFFX-r2-Bs-dap_3-5-ratio13.065866
Spike_AFFX-r2-Ec-bioB_5_signal11.151814
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.457766
NF1.000000
HZ4
Tau0.015000

Slide: Xiao_621-6_Gb-mutant_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 ("Xiao_621-6_Gb-mutant_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-6_Gb-mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_023077 (AZ)
Stock Code:
Age: 4-week-old
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:0.370447
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-ratio1.371397
Spike_AFFX-r2-Ec-bioB_3-5-ratio6.507521
Spike_AFFX-r2-Bs-dap_5_signal33.161434
NoiseAvg:3.36,Std:0.08,Min:3.1,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.533805
#P14434
Spike_AFFX-r2-Bs-phe_M_signal22.095871
Corner-Avg:12046,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.358454
Spike_AFFX-r2-Ec-bioB_3_signal9.993586
Spike_AFFX-r2-Bs-lys_M_signal14.916021
Spike_AFFX-r2-P1-cre_3_signal3240.240479
Spike_AFFX-r2-Bs-lys_3-5-ratio2.579919
Spike_AFFX-r2-Bs-dap_M_signal120.427223
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.375397
Spike_AFFX-r2-Ec-bioB_avg-signal6.629246
Spike_AFFX-r2-Bs-thr_avg-signal39.054562
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal653.195374
Spike_AFFX-r2-Bs-phe_5_signal16.608898
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal821.799683
RawQ2.766167
Spike_AFFX-r2-Bs-lys_5_signal16.955450
Signal(A)3.339097
%A35.238930
Signal(All)137.710403
Corner+Avg:203,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal135.690247
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal45.834179
Spike_AFFX-r2-Ec-bioD_avg-signal737.497559
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.279263
Spike_AFFX-r2-Bs-lys_avg-signal25.205055
Spike_AFFX-r2-P1-cre_avg-signal2801.484863
Spike_AFFX-r2-Ec-bioB_M_detectionM
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal87.392235
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-signal28.179651
Spike_AFFX-r2-Bs-dap_3_signal299.271912
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.258122
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal126.327393
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.743690
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.074116
Spike_AFFX-r2-Bs-thr_M_signal23.237646
Signal(P)215.455505
Spike_AFFX-r2-Bs-phe_3-5-ratio2.759616
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11778,Count:9
Spike_AFFX-r2-P1-cre_5_signal2362.729492
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8038
Signal(M)13.165746
BackgroundAvg:66.97,Std:0.59,Min:65.4,Max:69.2
Spike_AFFX-r2-Ec-bioC_avg-signal131.008820
Spike_AFFX-r2-Bs-dap_avg-signal150.953522
Spike_AFFX-r2-Bs-dap_3-5-ratio9.024697
Spike_AFFX-r2-Ec-bioB_5_signal1.535698
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.370447
NF1.000000
HZ4
Tau0.015000

Slide: Xiao_621-7_Gb-mutant_Rep3_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 ("Xiao_621-7_Gb-mutant_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-7_Gb-mutant_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_023077 (AZ)
Stock Code:
Age: 4-week-old
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:0.44785
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-ratio1.350946
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.719695
Spike_AFFX-r2-Bs-dap_5_signal41.799294
NoiseAvg:3.12,Std:0.10,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_signal7.161173
#P14429
Spike_AFFX-r2-Bs-phe_M_signal28.997211
Corner-Avg:11329,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.925971
Spike_AFFX-r2-Ec-bioB_3_signal8.034046
Spike_AFFX-r2-Bs-lys_M_signal17.903156
Spike_AFFX-r2-P1-cre_3_signal3494.129639
Spike_AFFX-r2-Bs-lys_3-5-ratio1.957747
Spike_AFFX-r2-Bs-dap_M_signal136.338120
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.777307
Spike_AFFX-r2-Ec-bioB_avg-signal10.041051
Spike_AFFX-r2-Bs-thr_avg-signal40.776249
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal643.536255
Spike_AFFX-r2-Bs-phe_5_signal18.837584
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal914.838623
RawQ2.639659
Spike_AFFX-r2-Bs-lys_5_signal18.407011
Signal(A)3.975673
%A35.217010
Signal(All)139.485962
Corner+Avg:181,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal164.663544
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.535095
Spike_AFFX-r2-Ec-bioD_avg-signal779.187439
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.257343
Spike_AFFX-r2-Bs-lys_avg-signal24.115480
Spike_AFFX-r2-P1-cre_avg-signal3040.281250
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.525647
Spike_AFFX-r2-Bs-thr_3_signal84.339325
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-signal32.789963
Spike_AFFX-r2-Bs-dap_3_signal351.747345
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.421581
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal143.113525
#M348
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.036274
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.150580
Spike_AFFX-r2-Bs-thr_M_signal30.828247
Signal(P)217.921829
Spike_AFFX-r2-Bs-phe_3-5-ratio2.682674
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11090,Count:9
Spike_AFFX-r2-P1-cre_5_signal2586.432617
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8033
Signal(M)15.356791
BackgroundAvg:63.83,Std:0.75,Min:61.9,Max:66.0
Spike_AFFX-r2-Ec-bioC_avg-signal153.888535
Spike_AFFX-r2-Bs-dap_avg-signal176.628250
Spike_AFFX-r2-Bs-dap_3-5-ratio8.415151
Spike_AFFX-r2-Ec-bioB_5_signal11.163134
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.447850
NF1.000000
HZ4
Tau0.015000

Slide: Xiao_621-8_Gb-mutant_Rep4_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 ("Xiao_621-8_Gb-mutant_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Xiao_621-8_Gb-mutant_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_023077 (AZ)
Stock Code:
Age: 4-week-old
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:0.475324
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-ratio1.397308
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.426510
Spike_AFFX-r2-Bs-dap_5_signal27.373543
NoiseAvg:2.97,Std:0.12,Min:2.7,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.692667
#P14335
Spike_AFFX-r2-Bs-phe_M_signal27.587852
Corner-Avg:10995,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal9.175831
Spike_AFFX-r2-Ec-bioB_3_signal13.924259
Spike_AFFX-r2-Bs-lys_M_signal15.658338
Spike_AFFX-r2-P1-cre_3_signal3868.660156
Spike_AFFX-r2-Bs-lys_3-5-ratio2.809378
Spike_AFFX-r2-Bs-dap_M_signal122.469269
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.918320
Spike_AFFX-r2-Ec-bioB_avg-signal10.953717
Spike_AFFX-r2-Bs-thr_avg-signal39.894749
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal772.464172
Spike_AFFX-r2-Bs-phe_5_signal20.835321
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal940.385925
RawQ2.427850
Spike_AFFX-r2-Bs-lys_5_signal14.950423
Signal(A)3.710820
%A35.642262
Signal(All)139.832550
Corner+Avg:178,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.057907
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.787558
Spike_AFFX-r2-Ec-bioD_avg-signal856.425049
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.845242
Spike_AFFX-r2-Bs-lys_avg-signal24.203382
Spike_AFFX-r2-P1-cre_avg-signal3318.656494
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal83.990997
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-signal26.736910
Spike_AFFX-r2-Bs-dap_3_signal290.721527
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.217385
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal164.557968
#M345
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.001385
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.960500
Spike_AFFX-r2-Bs-thr_M_signal28.000584
Signal(P)220.045395
Spike_AFFX-r2-Bs-phe_3-5-ratio1.525657
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10330,Count:9
Spike_AFFX-r2-P1-cre_5_signal2768.652832
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8130
Signal(M)14.668955
BackgroundAvg:61.08,Std:1.04,Min:58.7,Max:63.5
Spike_AFFX-r2-Ec-bioC_avg-signal161.307938
Spike_AFFX-r2-Bs-dap_avg-signal146.854782
Spike_AFFX-r2-Bs-dap_3-5-ratio10.620530
Spike_AFFX-r2-Ec-bioB_5_signal9.761064
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.475324
NF1.000000
HZ4
Tau0.015000


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