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Experiment: Analysis of gene expression in developing siliques of a mutant in bZIP67

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-606

The aim of this experiment is to analyse gene expression in developing seeds of a mutant in bZIP67 (At3g44460). Homozygous T-DNA insertion line SALK_085497 (N666597) and wild type plants were grown on soil to maturity in a growth chamber set to: 16 h light (21oC, 150 µmol m-2 s-1) / 8 h dark (18oC). Total RNA was prepared from whole siliques containing developing seeds at stage 8 to 9.

About the Experimenter

Name:Dr Peter Eastmond
Head of Lab Name:Dr Peter Eastmond
Lab:
Address:Warwick HRI , University of Warwick
Wellesbourne, Warwick, Warwickshire, CV35 9EF, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 02476575096

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:6
 
Experimental Parameters:
parameter gene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Eastmond: Analysis of gene expression in developing siliques of a mutant in bZIP67

Slide: Eastmond_606-1_WT_silique_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 ("Eastmond_606-1_WT_silique_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: Eastmond_606-1_WT_silique_Rep1_ATH1
Organism: Arabidopsis thaliana
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:0.434651
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-ratio1.174891
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.951096
Spike_AFFX-r2-Bs-dap_5_signal51.065434
NoiseAvg:3.15,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_signal16.327055
#P14857
Spike_AFFX-r2-Bs-phe_M_signal46.184265
Corner-Avg:8578,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal65.173294
Spike_AFFX-r2-Ec-bioB_3_signal49.280746
Spike_AFFX-r2-Bs-lys_M_signal39.930496
Spike_AFFX-r2-P1-cre_3_signal3060.010010
Spike_AFFX-r2-Bs-lys_3-5-ratio2.069726
Spike_AFFX-r2-Bs-dap_M_signal260.341797
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.148987
Spike_AFFX-r2-Ec-bioB_avg-signal55.422913
Spike_AFFX-r2-Bs-thr_avg-signal123.675636
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal569.796631
Spike_AFFX-r2-Bs-phe_5_signal36.945572
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal778.798889
RawQ2.616458
Spike_AFFX-r2-Bs-lys_5_signal39.204830
Signal(A)3.993128
%A33.200352
Signal(All)140.108398
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal149.720535
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal95.248497
Spike_AFFX-r2-Ec-bioD_avg-signal674.297729
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.133713
Spike_AFFX-r2-Bs-lys_avg-signal53.426193
Spike_AFFX-r2-P1-cre_avg-signal2832.257813
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.665936
Spike_AFFX-r2-Bs-thr_3_signal296.319519
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-signal59.459446
Spike_AFFX-r2-Bs-dap_3_signal551.482300
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.366802
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal145.506531
#M380
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal81.143257
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.028961
Spike_AFFX-r2-Bs-thr_M_signal58.380329
Signal(P)212.676224
Spike_AFFX-r2-Bs-phe_3-5-ratio2.578076
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6324,Count:9
Spike_AFFX-r2-P1-cre_5_signal2604.505615
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7573
Signal(M)15.530931
BackgroundAvg:62.53,Std:0.60,Min:60.7,Max:63.9
Spike_AFFX-r2-Ec-bioC_avg-signal147.613525
Spike_AFFX-r2-Bs-dap_avg-signal287.629852
Spike_AFFX-r2-Bs-dap_3-5-ratio10.799522
Spike_AFFX-r2-Ec-bioB_5_signal51.814693
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.434651
NF1.000000
HZ4
Tau0.015000

Slide: Eastmond_606-2_WT_silique_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 ("Eastmond_606-2_WT_silique_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: Eastmond_606-2_WT_silique_Rep2_ATH1
Organism: Arabidopsis thaliana
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:0.381916
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-ratio1.093780
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.201102
Spike_AFFX-r2-Bs-dap_5_signal35.939209
NoiseAvg:3.13,Std:0.11,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_signal11.111681
#P15115
Spike_AFFX-r2-Bs-phe_M_signal39.217045
Corner-Avg:8413,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal62.592129
Spike_AFFX-r2-Ec-bioB_3_signal50.125553
Spike_AFFX-r2-Bs-lys_M_signal25.291506
Spike_AFFX-r2-P1-cre_3_signal2763.085449
Spike_AFFX-r2-Bs-lys_3-5-ratio1.920830
Spike_AFFX-r2-Bs-dap_M_signal239.616821
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio20.192127
Spike_AFFX-r2-Ec-bioB_avg-signal51.483547
Spike_AFFX-r2-Bs-thr_avg-signal96.289940
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal498.518280
Spike_AFFX-r2-Bs-phe_5_signal25.602617
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal757.501038
RawQ2.758818
Spike_AFFX-r2-Bs-lys_5_signal30.185223
Signal(A)3.351904
%A32.156948
Signal(All)139.519394
Corner+Avg:149,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal129.753021
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal71.110252
Spike_AFFX-r2-Ec-bioD_avg-signal628.009644
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.264793
Spike_AFFX-r2-Bs-lys_avg-signal37.819138
Spike_AFFX-r2-P1-cre_avg-signal2644.632568
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal224.368484
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-signal45.309971
Spike_AFFX-r2-Bs-dap_3_signal512.984680
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.519505
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal129.087250
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.980686
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.005158
Spike_AFFX-r2-Bs-thr_M_signal53.389633
Signal(P)208.604370
Spike_AFFX-r2-Bs-phe_3-5-ratio2.777460
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6883,Count:9
Spike_AFFX-r2-P1-cre_5_signal2526.179688
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7335
Signal(M)13.322907
BackgroundAvg:64.46,Std:0.60,Min:62.6,Max:66.0
Spike_AFFX-r2-Ec-bioC_avg-signal129.420135
Spike_AFFX-r2-Bs-dap_avg-signal262.846893
Spike_AFFX-r2-Bs-dap_3-5-ratio14.273678
Spike_AFFX-r2-Ec-bioB_5_signal41.732960
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.381916
NF1.000000
HZ4
Tau0.015000

Slide: Eastmond_606-3_WT_silique_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 ("Eastmond_606-3_WT_silique_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: Eastmond_606-3_WT_silique_Rep3_ATH1
Organism: Arabidopsis thaliana
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:0.550823
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-ratio1.123130
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.299303
Spike_AFFX-r2-Bs-dap_5_signal62.353130
NoiseAvg:2.95,Std:0.20,Min:2.5,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.972633
#P14512
Spike_AFFX-r2-Bs-phe_M_signal41.343208
Corner-Avg:8280,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal76.385109
Spike_AFFX-r2-Ec-bioB_3_signal68.263069
Spike_AFFX-r2-Bs-lys_M_signal38.517033
Spike_AFFX-r2-P1-cre_3_signal3522.898193
Spike_AFFX-r2-Bs-lys_3-5-ratio2.045543
Spike_AFFX-r2-Bs-dap_M_signal356.925201
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.839565
Spike_AFFX-r2-Ec-bioB_avg-signal65.728798
Spike_AFFX-r2-Bs-thr_avg-signal159.406174
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal613.619690
Spike_AFFX-r2-Bs-phe_5_signal46.276691
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal821.100342
RawQ2.521247
Spike_AFFX-r2-Bs-lys_5_signal49.958668
Signal(A)4.773026
%A34.318283
Signal(All)142.734543
Corner+Avg:140,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal197.501282
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal135.033081
Spike_AFFX-r2-Ec-bioD_avg-signal717.359985
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.621220
Spike_AFFX-r2-Bs-lys_avg-signal63.556107
Spike_AFFX-r2-P1-cre_avg-signal3329.789063
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.060500
Spike_AFFX-r2-Bs-thr_3_signal356.303101
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-signal74.217659
Spike_AFFX-r2-Bs-dap_3_signal768.985229
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.338126
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal171.101532
#M470
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal102.192619
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.154293
Spike_AFFX-r2-Bs-thr_M_signal101.942810
Signal(P)221.196503
Spike_AFFX-r2-Bs-phe_3-5-ratio2.917950
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7206,Count:9
Spike_AFFX-r2-P1-cre_5_signal3136.680176
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7828
Signal(M)17.888937
BackgroundAvg:59.50,Std:1.17,Min:56.4,Max:61.6
Spike_AFFX-r2-Ec-bioC_avg-signal184.301407
Spike_AFFX-r2-Bs-dap_avg-signal396.087860
Spike_AFFX-r2-Bs-dap_3-5-ratio12.332745
Spike_AFFX-r2-Ec-bioB_5_signal52.538204
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.550823
NF1.000000
HZ4
Tau0.015000

Slide: Eastmond_606-4_Mutant_silique_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 ("Eastmond_606-4_Mutant_silique_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: Eastmond_606-4_Mutant_silique_Rep1_ATH1
Organism: Arabidopsis thaliana
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:0.396989
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-ratio1.189798
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.314360
Spike_AFFX-r2-Bs-dap_5_signal65.089455
NoiseAvg:3.14,Std:0.07,Min:2.8,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_signal17.410591
#P15039
Spike_AFFX-r2-Bs-phe_M_signal50.233067
Corner-Avg:7871,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal60.422939
Spike_AFFX-r2-Ec-bioB_3_signal48.541283
Spike_AFFX-r2-Bs-lys_M_signal35.993671
Spike_AFFX-r2-P1-cre_3_signal2844.242188
Spike_AFFX-r2-Bs-lys_3-5-ratio1.573412
Spike_AFFX-r2-Bs-dap_M_signal352.752899
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio19.512056
Spike_AFFX-r2-Ec-bioB_avg-signal48.631908
Spike_AFFX-r2-Bs-thr_avg-signal146.698517
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal528.841675
Spike_AFFX-r2-Bs-phe_5_signal46.339695
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal801.398987
RawQ2.637599
Spike_AFFX-r2-Bs-lys_5_signal49.484901
Signal(A)3.853287
%A32.327927
Signal(All)138.383636
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal139.451202
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal104.740288
Spike_AFFX-r2-Ec-bioD_avg-signal665.120361
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.931610
Spike_AFFX-r2-Bs-lys_avg-signal54.446247
Spike_AFFX-r2-P1-cre_avg-signal2617.384277
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.740465
Spike_AFFX-r2-Bs-thr_3_signal339.716431
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-signal67.104347
Spike_AFFX-r2-Bs-dap_3_signal712.553528
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.515386
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal148.683334
#M397
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal77.860161
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.937907
Spike_AFFX-r2-Bs-thr_M_signal82.968536
Signal(P)207.629333
Spike_AFFX-r2-Bs-phe_3-5-ratio2.260271
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7155,Count:9
Spike_AFFX-r2-P1-cre_5_signal2390.526123
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7374
Signal(M)14.052889
BackgroundAvg:61.41,Std:0.59,Min:59.5,Max:63.2
Spike_AFFX-r2-Ec-bioC_avg-signal144.067261
Spike_AFFX-r2-Bs-dap_avg-signal376.798615
Spike_AFFX-r2-Bs-dap_3-5-ratio10.947296
Spike_AFFX-r2-Ec-bioB_5_signal36.931496
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.396989
NF1.000000
HZ4
Tau0.015000

Slide: Eastmond_606-5_Mutant_silique_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 ("Eastmond_606-5_Mutant_silique_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: Eastmond_606-5_Mutant_silique_Rep2_ATH1
Organism: Arabidopsis thaliana
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:0.406964
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-ratio1.187205
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.856349
Spike_AFFX-r2-Bs-dap_5_signal65.629837
NoiseAvg:3.25,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_signal20.598856
#P14935
Spike_AFFX-r2-Bs-phe_M_signal42.461441
Corner-Avg:7691,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal56.623379
Spike_AFFX-r2-Ec-bioB_3_signal38.880550
Spike_AFFX-r2-Bs-lys_M_signal33.577435
Spike_AFFX-r2-P1-cre_3_signal2762.357666
Spike_AFFX-r2-Bs-lys_3-5-ratio1.130520
Spike_AFFX-r2-Bs-dap_M_signal289.785645
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.677253
Spike_AFFX-r2-Ec-bioB_avg-signal46.968872
Spike_AFFX-r2-Bs-thr_avg-signal119.177940
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal421.251801
Spike_AFFX-r2-Bs-phe_5_signal37.031673
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal602.209290
RawQ2.625884
Spike_AFFX-r2-Bs-lys_5_signal43.446404
Signal(A)3.911556
%A32.989918
Signal(All)137.271103
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal110.885841
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal111.407570
Spike_AFFX-r2-Ec-bioD_avg-signal511.730530
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.475670
Spike_AFFX-r2-Bs-lys_avg-signal42.046963
Spike_AFFX-r2-P1-cre_avg-signal2544.565674
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.534415
Spike_AFFX-r2-Bs-thr_3_signal261.136902
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-signal63.633564
Spike_AFFX-r2-Bs-dap_3_signal577.149719
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.429571
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal132.454880
#M350
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.117046
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.837159
Spike_AFFX-r2-Bs-thr_M_signal75.798058
Signal(P)207.330185
Spike_AFFX-r2-Bs-phe_3-5-ratio3.008440
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7114,Count:9
Spike_AFFX-r2-P1-cre_5_signal2326.773682
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7525
Signal(M)14.980922
BackgroundAvg:67.07,Std:0.71,Min:65.7,Max:69.1
Spike_AFFX-r2-Ec-bioC_avg-signal121.670364
Spike_AFFX-r2-Bs-dap_avg-signal310.855072
Spike_AFFX-r2-Bs-dap_3-5-ratio8.794014
Spike_AFFX-r2-Ec-bioB_5_signal45.402687
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.406964
NF1.000000
HZ4
Tau0.015000

Slide: Eastmond_606-6_Mutant_silique_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 ("Eastmond_606-6_Mutant_silique_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: Eastmond_606-6_Mutant_silique_Rep3_ATH1
Organism: Arabidopsis thaliana
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:0.650635
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-ratio1.039348
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.494357
Spike_AFFX-r2-Bs-dap_5_signal76.464935
NoiseAvg:2.41,Std:0.13,Min:2.1,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.055813
#P14559
Spike_AFFX-r2-Bs-phe_M_signal54.773693
Corner-Avg:8075,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal105.580879
Spike_AFFX-r2-Ec-bioB_3_signal96.312469
Spike_AFFX-r2-Bs-lys_M_signal40.856880
Spike_AFFX-r2-P1-cre_3_signal3689.264160
Spike_AFFX-r2-Bs-lys_3-5-ratio1.990320
Spike_AFFX-r2-Bs-dap_M_signal352.647003
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.452576
Spike_AFFX-r2-Ec-bioB_avg-signal88.781372
Spike_AFFX-r2-Bs-thr_avg-signal157.155441
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal641.385315
Spike_AFFX-r2-Bs-phe_5_signal56.467224
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1158.299561
RawQ2.244471
Spike_AFFX-r2-Bs-lys_5_signal58.686260
Signal(A)5.010972
%A34.213066
Signal(All)142.940582
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal252.874374
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal136.762482
Spike_AFFX-r2-Ec-bioD_avg-signal899.842407
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.827271
Spike_AFFX-r2-Bs-lys_avg-signal72.115868
Spike_AFFX-r2-P1-cre_avg-signal3619.429932
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.959667
Spike_AFFX-r2-Bs-thr_3_signal351.628845
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-signal82.667801
Spike_AFFX-r2-Bs-dap_3_signal771.265930
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.805934
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal252.726486
#M447
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal116.804451
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.000585
Spike_AFFX-r2-Bs-thr_M_signal100.781670
Signal(P)220.749374
Spike_AFFX-r2-Bs-phe_3-5-ratio2.421980
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6721,Count:9
Spike_AFFX-r2-P1-cre_5_signal3549.595703
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7804
Signal(M)16.731218
BackgroundAvg:51.31,Std:0.75,Min:49.9,Max:52.8
Spike_AFFX-r2-Ec-bioC_avg-signal252.800430
Spike_AFFX-r2-Bs-dap_avg-signal400.125977
Spike_AFFX-r2-Bs-dap_3-5-ratio10.086531
Spike_AFFX-r2-Ec-bioB_5_signal64.450790
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.650635
NF1.000000
HZ4
Tau0.015000


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