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Experiment: Microarray analysis wild type versus mutant

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-608

Phospholipid biosynthesis is essential for the construction of most eukaryotic cell membranes, but how this process isregulated in plants remains poorly understood. Here, we show that in Arabidopsis thaliana, two Mg2+-dependentphosphatidic acid phosphohydrolases called PAH1 and PAH2 act redundantly to repress phospholipid biosynthesis atthe endoplasmic reticulum (ER). Leaves from pah1 pah2 double mutants contain ;1.8-fold more phospholipid than the wildtype and exhibit gross changes in ER morphology, which are consistent with massive membrane overexpansion. The netrate of incorporation of [methyl-14C]choline into phosphatidylcholine (PC) is ;1.8-fold greater in the double mutant, and thetranscript abundance of several key genes that encode enzymes involved in phospholipid synthesis is increased. Inparticular, we show that PHOSPHORYLETHANOLAMINE N-METHYLTRANSFERASE1 (PEAMT1) is upregulated at the level oftranscription in pah1 pah2 leaves. PEAMT catalyzes the first committed step of choline synthesis in Arabidopsis and definesa variant pathway for PC synthesis not found in yeasts or mammals. Our data suggest that PAH1/2 play a regulatory role inphospholipid synthesis that is analogous to that described in Saccharomyces cerevisiae. However, the target enzymesdiffer, and key components of the signal transduction pathway do not appear to be conserved.

About the Experimenter

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

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

About this Experiment

Experiment Type: genetic_modification
Number of Slides:6
 
Experimental Parameters:
parameter genetic_modification
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Craddock: Microarray analysis wild type versus mutant

Slide: Craddock_608-1_WT_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 ("Craddock_608-1_WT_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: Craddock_608-1_WT_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:0.318785
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-ratio1.353897
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.214252
Spike_AFFX-r2-Bs-dap_5_signal24.032490
NoiseAvg:3.46,Std:0.11,Min:3.1,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_signal9.030953
#P14373
Spike_AFFX-r2-Bs-phe_M_signal27.341869
Corner-Avg:10145,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal38.593620
Spike_AFFX-r2-Ec-bioB_3_signal38.324459
Spike_AFFX-r2-Bs-lys_M_signal18.120031
Spike_AFFX-r2-P1-cre_3_signal3272.574951
Spike_AFFX-r2-Bs-lys_3-5-ratio1.435767
Spike_AFFX-r2-Bs-dap_M_signal162.931183
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.105097
Spike_AFFX-r2-Ec-bioB_avg-signal36.160084
Spike_AFFX-r2-Bs-thr_avg-signal60.769588
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal720.199402
Spike_AFFX-r2-Bs-phe_5_signal21.136959
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal913.146606
RawQ2.812257
Spike_AFFX-r2-Bs-lys_5_signal29.401402
Signal(A)3.149927
%A35.436211
Signal(All)136.631363
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal234.952240
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.229313
Spike_AFFX-r2-Ec-bioD_avg-signal816.672974
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.011837
Spike_AFFX-r2-Bs-lys_avg-signal29.911667
Spike_AFFX-r2-P1-cre_avg-signal2844.863770
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.551951
Spike_AFFX-r2-Bs-thr_3_signal136.413422
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal33.569382
Spike_AFFX-r2-Bs-dap_3_signal321.248993
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.267908
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal218.347504
#M354
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.213570
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.076047
Spike_AFFX-r2-Bs-thr_M_signal36.864380
Signal(P)214.743134
Spike_AFFX-r2-Bs-phe_3-5-ratio2.470995
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7462,Count:9
Spike_AFFX-r2-P1-cre_5_signal2417.152832
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8083
Signal(M)12.987472
BackgroundAvg:66.17,Std:0.61,Min:64.8,Max:68.2
Spike_AFFX-r2-Ec-bioC_avg-signal226.649872
Spike_AFFX-r2-Bs-dap_avg-signal169.404221
Spike_AFFX-r2-Bs-dap_3-5-ratio13.367279
Spike_AFFX-r2-Ec-bioB_5_signal31.562183
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.318785
NF1.000000
HZ4
Tau0.015000

Slide: Craddock_608-2_WT_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 ("Craddock_608-2_WT_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: Craddock_608-2_WT_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:0.456117
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-ratio1.476261
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.323222
Spike_AFFX-r2-Bs-dap_5_signal24.792564
NoiseAvg:3.07,Std:0.10,Min:2.7,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_signal7.623999
#P14102
Spike_AFFX-r2-Bs-phe_M_signal26.205589
Corner-Avg:8808,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal42.326180
Spike_AFFX-r2-Ec-bioB_3_signal32.818150
Spike_AFFX-r2-Bs-lys_M_signal19.362795
Spike_AFFX-r2-P1-cre_3_signal3629.702393
Spike_AFFX-r2-Bs-lys_3-5-ratio2.027503
Spike_AFFX-r2-Bs-dap_M_signal149.695206
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.849592
Spike_AFFX-r2-Ec-bioB_avg-signal33.315346
Spike_AFFX-r2-Bs-thr_avg-signal61.308567
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal709.624329
Spike_AFFX-r2-Bs-phe_5_signal16.782093
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal991.619934
RawQ2.756665
Spike_AFFX-r2-Bs-lys_5_signal23.405741
Signal(A)3.248052
%A36.707584
Signal(All)136.237167
Corner+Avg:169,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal227.097366
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.314499
Spike_AFFX-r2-Ec-bioD_avg-signal850.622131
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.823761
Spike_AFFX-r2-Bs-lys_avg-signal30.074585
Spike_AFFX-r2-P1-cre_avg-signal3044.208008
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal136.085266
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.434061
Spike_AFFX-r2-Bs-dap_3_signal341.559326
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.397387
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal196.390991
#M335
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.455223
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.156353
Spike_AFFX-r2-Bs-thr_M_signal40.216442
Signal(P)218.134933
Spike_AFFX-r2-Bs-phe_3-5-ratio2.342646
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6132,Count:9
Spike_AFFX-r2-P1-cre_5_signal2458.713379
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8373
Signal(M)12.642322
BackgroundAvg:63.02,Std:0.46,Min:61.7,Max:64.4
Spike_AFFX-r2-Ec-bioC_avg-signal211.744171
Spike_AFFX-r2-Bs-dap_avg-signal172.015686
Spike_AFFX-r2-Bs-dap_3-5-ratio13.776684
Spike_AFFX-r2-Ec-bioB_5_signal24.801702
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.456117
NF1.000000
HZ4
Tau0.015000

Slide: Craddock_608-3_WT_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 ("Craddock_608-3_WT_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: Craddock_608-3_WT_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:0.330266
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-ratio1.296882
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.276186
Spike_AFFX-r2-Bs-dap_5_signal12.920198
NoiseAvg:4.02,Std:0.15,Min:3.6,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.874360
#P14116
Spike_AFFX-r2-Bs-phe_M_signal19.396444
Corner-Avg:13128,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal30.980938
Spike_AFFX-r2-Ec-bioB_3_signal29.094213
Spike_AFFX-r2-Bs-lys_M_signal10.760062
Spike_AFFX-r2-P1-cre_3_signal2774.805176
Spike_AFFX-r2-Bs-lys_3-5-ratio3.103439
Spike_AFFX-r2-Bs-dap_M_signal75.373215
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio20.620001
Spike_AFFX-r2-Ec-bioB_avg-signal27.624308
Spike_AFFX-r2-Bs-thr_avg-signal38.057339
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal558.316101
Spike_AFFX-r2-Bs-phe_5_signal14.084306
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal799.147095
RawQ3.188472
Spike_AFFX-r2-Bs-lys_5_signal13.298626
Signal(A)3.366917
%A36.685665
Signal(All)135.283401
Corner+Avg:236,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal161.808090
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.079868
Spike_AFFX-r2-Ec-bioD_avg-signal678.731567
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.885139
Spike_AFFX-r2-Bs-lys_avg-signal21.776718
Spike_AFFX-r2-P1-cre_avg-signal2457.200928
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.429198
Spike_AFFX-r2-Bs-thr_3_signal79.889305
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.520205
Spike_AFFX-r2-Bs-dap_3_signal210.529526
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.431352
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal165.722061
#M326
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.271469
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.976382
Spike_AFFX-r2-Bs-thr_M_signal30.408354
Signal(P)216.308426
Spike_AFFX-r2-Bs-phe_3-5-ratio1.780696
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9749,Count:9
Spike_AFFX-r2-P1-cre_5_signal2139.596680
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8368
Signal(M)12.976260
BackgroundAvg:78.82,Std:0.88,Min:77.0,Max:81.2
Spike_AFFX-r2-Ec-bioC_avg-signal163.765076
Spike_AFFX-r2-Bs-dap_avg-signal99.607643
Spike_AFFX-r2-Bs-dap_3-5-ratio16.294605
Spike_AFFX-r2-Ec-bioB_5_signal22.797775
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.330266
NF1.000000
HZ4
Tau0.015000

Slide: Craddock_608-4_pah_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 ("Craddock_608-4_pah_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: Craddock_608-4_pah_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:0.365586
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-ratio1.391056
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.998290
Spike_AFFX-r2-Bs-dap_5_signal20.584412
NoiseAvg:3.79,Std:0.12,Min:3.5,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.615803
#P14187
Spike_AFFX-r2-Bs-phe_M_signal25.952393
Corner-Avg:9368,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal34.705154
Spike_AFFX-r2-Ec-bioB_3_signal25.400600
Spike_AFFX-r2-Bs-lys_M_signal16.644478
Spike_AFFX-r2-P1-cre_3_signal3280.566162
Spike_AFFX-r2-Bs-lys_3-5-ratio1.646869
Spike_AFFX-r2-Bs-dap_M_signal131.242447
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio20.141468
Spike_AFFX-r2-Ec-bioB_avg-signal28.516624
Spike_AFFX-r2-Bs-thr_avg-signal54.238972
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal583.918213
Spike_AFFX-r2-Bs-phe_5_signal14.984038
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal837.517090
RawQ3.168679
Spike_AFFX-r2-Bs-lys_5_signal19.726748
Signal(A)3.719129
%A36.264797
Signal(All)138.120621
Corner+Avg:178,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal183.646423
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.490864
Spike_AFFX-r2-Ec-bioD_avg-signal710.717651
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.196404
Spike_AFFX-r2-Bs-lys_avg-signal22.952868
Spike_AFFX-r2-P1-cre_avg-signal2819.447266
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.538799
Spike_AFFX-r2-Bs-thr_3_signal113.110512
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-signal25.809097
Spike_AFFX-r2-Bs-dap_3_signal257.765106
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.434305
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.996201
#M351
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.487377
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.009067
Spike_AFFX-r2-Bs-thr_M_signal43.990612
Signal(P)219.554031
Spike_AFFX-r2-Bs-phe_3-5-ratio2.435316
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6927,Count:9
Spike_AFFX-r2-P1-cre_5_signal2358.328613
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8272
Signal(M)14.113652
BackgroundAvg:77.56,Std:0.83,Min:75.2,Max:79.5
Spike_AFFX-r2-Ec-bioC_avg-signal182.821320
Spike_AFFX-r2-Bs-dap_avg-signal136.530655
Spike_AFFX-r2-Bs-dap_3-5-ratio12.522346
Spike_AFFX-r2-Ec-bioB_5_signal25.444117
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.365586
NF1.000000
HZ4
Tau0.015000

Slide: Craddock_608-5_pah_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 ("Craddock_608-5_pah_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: Craddock_608-5_pah_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:0.366165
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-ratio1.339313
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.264649
Spike_AFFX-r2-Bs-dap_5_signal22.504417
NoiseAvg:3.50,Std:0.22,Min:3.1,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.248730
#P14047
Spike_AFFX-r2-Bs-phe_M_signal24.929749
Corner-Avg:9599,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal33.644466
Spike_AFFX-r2-Ec-bioB_3_signal31.794130
Spike_AFFX-r2-Bs-lys_M_signal13.673787
Spike_AFFX-r2-P1-cre_3_signal2979.868652
Spike_AFFX-r2-Bs-lys_3-5-ratio1.517348
Spike_AFFX-r2-Bs-dap_M_signal122.326691
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.289505
Spike_AFFX-r2-Ec-bioB_avg-signal30.193094
Spike_AFFX-r2-Bs-thr_avg-signal42.389641
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal685.699036
Spike_AFFX-r2-Bs-phe_5_signal20.790693
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal905.127869
RawQ2.909441
Spike_AFFX-r2-Bs-lys_5_signal25.411634
Signal(A)3.304281
%A36.996933
Signal(All)136.654617
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal198.783188
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.638298
Spike_AFFX-r2-Ec-bioD_avg-signal795.413452
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.582638
Spike_AFFX-r2-Bs-lys_avg-signal25.881239
Spike_AFFX-r2-P1-cre_avg-signal2602.396484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.420430
Spike_AFFX-r2-Bs-thr_3_signal80.250488
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-signal29.119581
Spike_AFFX-r2-Bs-dap_3_signal260.775757
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.320007
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.694992
#M324
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.558296
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.137887
Spike_AFFX-r2-Bs-thr_M_signal41.669701
Signal(P)219.626892
Spike_AFFX-r2-Bs-phe_3-5-ratio2.002737
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7439,Count:9
Spike_AFFX-r2-P1-cre_5_signal2224.924072
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8439
Signal(M)12.678597
BackgroundAvg:72.88,Std:1.08,Min:70.2,Max:75.5
Spike_AFFX-r2-Ec-bioC_avg-signal186.739090
Spike_AFFX-r2-Bs-dap_avg-signal135.202286
Spike_AFFX-r2-Bs-dap_3-5-ratio11.587759
Spike_AFFX-r2-Ec-bioB_5_signal25.140684
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.366165
NF1.000000
HZ4
Tau0.015000

Slide: Craddock_608-6_pah_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 ("Craddock_608-6_pah_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: Craddock_608-6_pah_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:0.372895
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-ratio1.384802
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.649524
Spike_AFFX-r2-Bs-dap_5_signal22.298365
NoiseAvg:3.75,Std:0.14,Min:3.5,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal1.452594
#P14115
Spike_AFFX-r2-Bs-phe_M_signal27.812475
Corner-Avg:12673,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal35.422611
Spike_AFFX-r2-Ec-bioB_3_signal20.296461
Spike_AFFX-r2-Bs-lys_M_signal15.602366
Spike_AFFX-r2-P1-cre_3_signal3226.320068
Spike_AFFX-r2-Bs-lys_3-5-ratio1.607187
Spike_AFFX-r2-Bs-dap_M_signal123.675705
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio81.727448
Spike_AFFX-r2-Ec-bioB_avg-signal28.989096
Spike_AFFX-r2-Bs-thr_avg-signal52.923553
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal618.740784
Spike_AFFX-r2-Bs-phe_5_signal18.440443
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal923.923157
RawQ3.118701
Spike_AFFX-r2-Bs-lys_5_signal25.577011
Signal(A)3.672515
%A36.637440
Signal(All)139.246033
Corner+Avg:223,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal189.870163
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.606277
Spike_AFFX-r2-Ec-bioD_avg-signal771.331970
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.880753
Spike_AFFX-r2-Bs-lys_avg-signal27.428808
Spike_AFFX-r2-P1-cre_avg-signal2778.062988
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal118.716789
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-signal32.953068
Spike_AFFX-r2-Bs-dap_3_signal254.726685
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.493231
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal184.082901
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.107044
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.031438
Spike_AFFX-r2-Bs-thr_M_signal38.601280
Signal(P)222.507385
Spike_AFFX-r2-Bs-phe_3-5-ratio2.852767
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9729,Count:9
Spike_AFFX-r2-P1-cre_5_signal2329.805664
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8357
Signal(M)14.257888
BackgroundAvg:77.50,Std:0.66,Min:75.8,Max:79.0
Spike_AFFX-r2-Ec-bioC_avg-signal186.976532
Spike_AFFX-r2-Bs-dap_avg-signal133.566925
Spike_AFFX-r2-Bs-dap_3-5-ratio11.423559
Spike_AFFX-r2-Ec-bioB_5_signal31.248217
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.372895
NF1.000000
HZ4
Tau0.015000


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