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Experiment: The effects of mutants in stress response pathways on gene expression during senescence

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-52

Many signalling pathways are involved in controlling gene expression during plant senescence. Pathways involving SA, JA and ethylene have a role in senescence but none are essential for the senescence process to occur. The aim of this experiment is to classify senescence-enhanced genes into groups depending on the signalling pathways that regulate them. This will provide useful information on the relative importance of each signalling pathway during senescence and allow us to separate potential senescence-specific genes and pathways from the stress response pathways.Mutants in genes in the ethylene pathway (ein2) and the jasmonate pathway (coi1) and the NahG transgenic plant which is defective in the salicylic acid pathway will be grown until the mid flowering stage. Fully developed green and partially senescent leaves will be harvested from the plants at this stage. In addition, two different lines of Arabidopsis (Col5 glabrous and Col-0) will be grown as controls. Leaves will be harvested from the two control plants before flowering (green) and at mid flowering as above. The control plants will be harvested at two stages to identify the senescence- enhanced genes. The effects of each mutation on the senescence related expression of these genes will then be studied.Mutant RNAs will be isolated in duplicate. The two control accessions will act as replicates for the wild type. Two wild type accessions will be used to reduce possible differences that could be observed the mutants due to slight differences in background.

About the Experimenter

Name:Dr Vicky Buchanan-Wollaston
Head of Lab Name:
Lab:
Institute: Horticulture Research International
Address:Horticulture Research International
Wellesbourne
Warwick
Postcode: CV35 9EF
Country: UK
 
Telephone Number: 01789 470382
Fax Number: 01789 470552

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

About this Experiment

Experiment Type: genetic_modification_design; development_or_differentiation_design
Number of Slides:10
 
Experimental Parameters:
parameterdevelopmental_stage
parameter gene_knock_out
Quality Control Measures Taken:
no-plants-pooledleaves from 10-20 plants per pool
References:
 
Other Information:
ArrayExpressAccessionE-NASC-17

Slides in this Experiment

Hybridisation Set: Buchanan-Wollaston_genome

Slide: Buchanan-Wollaston_A-1-bwoll-C0G_SLD

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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 ("Buchanan-Wollaston_A-1-bwoll-C0G_SRC") 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: Buchanan-Wollaston_A-1-bwoll-C0G_SRC
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N933
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.9
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.734776
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-ratio1.048502
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.894467
Spike_AFFX-r2-Bs-dap_5_signal2.195606
NoiseAvg:3.55,Std:0.21,Min:3.1,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_signal38.476757
#P11109
Spike_AFFX-r2-Bs-phe_M_signal2.918290
Corner-Avg:10608,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal123.295036
Spike_AFFX-r2-Ec-bioB_3_signal108.682518
Spike_AFFX-r2-Bs-lys_M_signal6.574436
Spike_AFFX-r2-P1-cre_3_signal5368.328613
Spike_AFFX-r2-Bs-lys_3-5-ratio0.888757
Spike_AFFX-r2-Bs-dap_M_signal1.781643
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.061596
Spike_AFFX-r2-Ec-bioB_avg-signal117.827614
Spike_AFFX-r2-Bs-thr_avg-signal18.049271
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal1222.265503
Spike_AFFX-r2-Bs-phe_5_signal4.649953
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1500.924927
RawQ2.749003
Spike_AFFX-r2-Bs-lys_5_signal6.384809
Signal(A)20.336395
%A47.404648
Signal(All)146.519669
Corner+Avg:163,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal384.222137
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal11.133926
Spike_AFFX-r2-Ec-bioD_avg-signal1361.595215
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P48.702324
Spike_AFFX-r2-Bs-lys_avg-signal6.211264
Spike_AFFX-r2-P1-cre_avg-signal5244.163086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.893029
Spike_AFFX-r2-Bs-thr_3_signal2.370004
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal6.234056
Spike_AFFX-r2-Bs-dap_3_signal5.698948
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.227986
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal337.014526
#M888
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal5.674545
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.140076
Spike_AFFX-r2-Bs-thr_M_signal13.301052
Signal(P)277.019684
Spike_AFFX-r2-Bs-phe_3-5-ratio2.394417
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10762,Count:9
Spike_AFFX-r2-P1-cre_5_signal5119.997559
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10813
Signal(M)50.455387
BackgroundAvg:65.19,Std:1.21,Min:63.2,Max:69.4
Spike_AFFX-r2-Ec-bioC_avg-signal360.618347
Spike_AFFX-r2-Bs-dap_avg-signal3.225399
Spike_AFFX-r2-Bs-dap_3-5-ratio2.595615
Spike_AFFX-r2-Ec-bioB_5_signal121.505280
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.734776
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-2-bwoll-C5G_SLD

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 ("Buchanan-Wollaston_A-2-bwoll-C5G_SRC") 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: Buchanan-Wollaston_A-2-bwoll-C5G_SRC
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code: N1644
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.9
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.637981
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-ratio1.076740
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.095550
Spike_AFFX-r2-Bs-dap_5_signal1.265960
NoiseAvg:4.02,Std:0.42,Min:3.4,Max:6.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.307667
#P11955
Spike_AFFX-r2-Bs-phe_M_signal6.142262
Corner-Avg:13261,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal120.218842
Spike_AFFX-r2-Ec-bioB_3_signal108.396706
Spike_AFFX-r2-Bs-lys_M_signal9.890697
Spike_AFFX-r2-P1-cre_3_signal5041.986816
Spike_AFFX-r2-Bs-lys_3-5-ratio0.880545
Spike_AFFX-r2-Bs-dap_M_signal0.365969
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.185959
Spike_AFFX-r2-Ec-bioB_avg-signal109.186073
Spike_AFFX-r2-Bs-thr_avg-signal5.016195
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal1079.884033
Spike_AFFX-r2-Bs-phe_5_signal2.947917
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1362.824951
RawQ2.818485
Spike_AFFX-r2-Bs-lys_5_signal9.865349
Signal(A)17.724531
%A43.770275
Signal(All)145.032394
Corner+Avg:213,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal367.356903
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal7.763209
Spike_AFFX-r2-Ec-bioD_avg-signal1221.354492
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P52.411224
Spike_AFFX-r2-Bs-lys_avg-signal9.480977
Spike_AFFX-r2-P1-cre_avg-signal4862.312988
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.818501
Spike_AFFX-r2-Bs-thr_3_signal1.916798
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal5.617795
Spike_AFFX-r2-Bs-dap_3_signal0.936595
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.262010
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal336.820343
#M871
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal8.686886
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.090661
Spike_AFFX-r2-Bs-thr_M_signal2.824118
Signal(P)258.757233
Spike_AFFX-r2-Bs-phe_3-5-ratio2.633456
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10813,Count:9
Spike_AFFX-r2-P1-cre_5_signal4682.639160
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9984
Signal(M)43.380516
BackgroundAvg:67.27,Std:1.61,Min:64.6,Max:72.8
Spike_AFFX-r2-Ec-bioC_avg-signal352.088623
Spike_AFFX-r2-Bs-dap_avg-signal0.856174
Spike_AFFX-r2-Bs-dap_3-5-ratio0.739830
Spike_AFFX-r2-Ec-bioB_5_signal98.942703
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.637981
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-3-bwoll-C0S_SLD

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 ("Buchanan-Wollaston_A-3-bwoll-C0S_SRC") 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: Buchanan-Wollaston_A-3-bwoll-C0S_SRC
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N933
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.420116
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.983467
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.700534
Spike_AFFX-r2-Bs-dap_5_signal1.504427
NoiseAvg:3.92,Std:0.18,Min:3.4,Max:4.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.067846
#P12653
Spike_AFFX-r2-Bs-phe_M_signal0.787683
Corner-Avg:12757,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.826309
Spike_AFFX-r2-Ec-bioB_3_signal54.224873
Spike_AFFX-r2-Bs-lys_M_signal3.572927
Spike_AFFX-r2-P1-cre_3_signal2944.468262
Spike_AFFX-r2-Bs-lys_3-5-ratio1.194622
Spike_AFFX-r2-Bs-dap_M_signal1.763004
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.581117
Spike_AFFX-r2-Ec-bioB_avg-signal66.485420
Spike_AFFX-r2-Bs-thr_avg-signal11.261363
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal620.299072
Spike_AFFX-r2-Bs-phe_5_signal2.696308
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal752.953735
RawQ2.914714
Spike_AFFX-r2-Bs-lys_5_signal5.105352
Signal(A)10.820965
%A41.836914
Signal(All)130.852051
Corner+Avg:186,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal227.377716
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal5.319822
Spike_AFFX-r2-Ec-bioD_avg-signal686.626404
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P55.471283
Spike_AFFX-r2-Bs-lys_avg-signal4.925748
Spike_AFFX-r2-P1-cre_avg-signal2969.218018
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.691802
Spike_AFFX-r2-Bs-thr_3_signal5.850593
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.934605
Spike_AFFX-r2-Bs-dap_3_signal2.229650
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.213856
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.120239
#M614
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal6.098965
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.255396
Spike_AFFX-r2-Bs-thr_M_signal17.865652
Signal(P)226.210846
Spike_AFFX-r2-Bs-phe_3-5-ratio1.973002
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10645,Count:9
Spike_AFFX-r2-P1-cre_5_signal2993.967773
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9543
Signal(M)31.311079
BackgroundAvg:72.91,Std:2.22,Min:68.5,Max:79.8
Spike_AFFX-r2-Ec-bioC_avg-signal204.248978
Spike_AFFX-r2-Bs-dap_avg-signal1.832360
Spike_AFFX-r2-Bs-dap_3-5-ratio1.482060
Spike_AFFX-r2-Ec-bioB_5_signal77.405083
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.420116
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-4-bwoll-C5S_SLD

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 ("Buchanan-Wollaston_A-4-bwoll-C5S_SRC") 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: Buchanan-Wollaston_A-4-bwoll-C5S_SRC
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N1644
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.464038
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-ratio1.064371
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.927368
Spike_AFFX-r2-Bs-dap_5_signal6.770776
NoiseAvg:4.54,Std:0.31,Min:3.8,Max:5.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.521102
#P13420
Spike_AFFX-r2-Bs-phe_M_signal0.524486
Corner-Avg:13102,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.558113
Spike_AFFX-r2-Ec-bioB_3_signal69.110893
Spike_AFFX-r2-Bs-lys_M_signal4.660196
Spike_AFFX-r2-P1-cre_3_signal3476.275146
Spike_AFFX-r2-Bs-lys_3-5-ratio1.797374
Spike_AFFX-r2-Bs-dap_M_signal0.194833
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.161130
Spike_AFFX-r2-Ec-bioB_avg-signal80.064224
Spike_AFFX-r2-Bs-thr_avg-signal10.575913
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal690.809509
Spike_AFFX-r2-Bs-phe_5_signal2.300084
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal788.647400
RawQ3.033244
Spike_AFFX-r2-Bs-lys_5_signal3.542002
Signal(A)16.695700
%A37.733452
Signal(All)130.142746
Corner+Avg:168,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.309631
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal2.757631
Spike_AFFX-r2-Ec-bioD_avg-signal739.728455
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P58.833843
Spike_AFFX-r2-Bs-lys_avg-signal4.856166
Spike_AFFX-r2-P1-cre_avg-signal3371.156250
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.432705
Spike_AFFX-r2-Bs-thr_3_signal2.500919
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal1.860734
Spike_AFFX-r2-Bs-dap_3_signal3.645749
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.141628
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal171.786713
#M783
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal6.366301
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.381420
Spike_AFFX-r2-Bs-thr_M_signal13.705719
Signal(P)208.366959
Spike_AFFX-r2-Bs-phe_3-5-ratio1.198926
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10025,Count:9
Spike_AFFX-r2-P1-cre_5_signal3266.037109
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8607
Signal(M)36.489975
BackgroundAvg:75.33,Std:2.38,Min:71.7,Max:83.7
Spike_AFFX-r2-Ec-bioC_avg-signal204.548172
Spike_AFFX-r2-Bs-dap_avg-signal3.537120
Spike_AFFX-r2-Bs-dap_3-5-ratio0.538454
Spike_AFFX-r2-Ec-bioB_5_signal74.523666
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.464038
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-5-bwoll-NG1_SLD

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 ("Buchanan-Wollaston_A-5-bwoll-NG1_SRC") 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: Buchanan-Wollaston_A-5-bwoll-NG1_SRC
Organism: Arabidopsis thaliana
Alias: NahG
Stock Code:
Genetic Background: Columbia
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Genetic Variation: NahG transgenic
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.629044
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-ratio1.111145
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.089261
Spike_AFFX-r2-Bs-dap_5_signal5.685140
NoiseAvg:3.74,Std:0.19,Min:3.3,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_signal23.310364
#P11434
Spike_AFFX-r2-Bs-phe_M_signal0.865561
Corner-Avg:12438,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.485062
Spike_AFFX-r2-Ec-bioB_3_signal80.088493
Spike_AFFX-r2-Bs-lys_M_signal4.751813
Spike_AFFX-r2-P1-cre_3_signal4157.553711
Spike_AFFX-r2-Bs-lys_3-5-ratio0.701905
Spike_AFFX-r2-Bs-dap_M_signal1.971553
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.292452
Spike_AFFX-r2-Ec-bioB_avg-signal79.366371
Spike_AFFX-r2-Bs-thr_avg-signal13.455860
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal697.731445
Spike_AFFX-r2-Bs-phe_5_signal3.507614
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal829.764709
RawQ2.841990
Spike_AFFX-r2-Bs-lys_5_signal9.958770
Signal(A)20.129288
%A45.909687
Signal(All)136.122421
Corner+Avg:154,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal276.117401
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal2.543449
Spike_AFFX-r2-Ec-bioD_avg-signal763.748047
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P50.127136
Spike_AFFX-r2-Bs-lys_avg-signal7.233565
Spike_AFFX-r2-P1-cre_avg-signal3949.618896
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.963174
Spike_AFFX-r2-Bs-thr_3_signal6.817158
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.305542
Spike_AFFX-r2-Bs-dap_3_signal0.672037
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.189232
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal233.574692
#M904
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal6.990112
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.182137
Spike_AFFX-r2-Bs-thr_M_signal10.240059
Signal(P)249.276413
Spike_AFFX-r2-Bs-phe_3-5-ratio0.725122
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10411,Count:9
Spike_AFFX-r2-P1-cre_5_signal3741.684082
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10472
Signal(M)48.597233
BackgroundAvg:67.71,Std:0.96,Min:65.2,Max:71.0
Spike_AFFX-r2-Ec-bioC_avg-signal254.846039
Spike_AFFX-r2-Bs-dap_avg-signal2.776243
Spike_AFFX-r2-Bs-dap_3-5-ratio0.118209
Spike_AFFX-r2-Ec-bioB_5_signal73.525558
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.629044
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-6-bwoll-NG2_SLD

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 ("Buchanan-Wollaston_A-5-bwoll-NG2_SRC") 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: Buchanan-Wollaston_A-5-bwoll-NG2_SRC
Organism: Arabidopsis thaliana
Alias: NahG
Stock Code:
Genetic Background: Columbia
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Genetic Variation: NahG transgenic
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.457951
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-ratio1.010350
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.031230
Spike_AFFX-r2-Bs-dap_5_signal6.902372
NoiseAvg:4.93,Std:0.27,Min:4.3,Max:5.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.193363
#P11986
Spike_AFFX-r2-Bs-phe_M_signal3.593283
Corner-Avg:12891,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal47.717960
Spike_AFFX-r2-Ec-bioB_3_signal71.988281
Spike_AFFX-r2-Bs-lys_M_signal1.206533
Spike_AFFX-r2-P1-cre_3_signal3157.083984
Spike_AFFX-r2-Bs-lys_3-5-ratio1.583782
Spike_AFFX-r2-Bs-dap_M_signal1.870195
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.078040
Spike_AFFX-r2-Ec-bioB_avg-signal63.171467
Spike_AFFX-r2-Bs-thr_avg-signal10.079379
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal592.146301
Spike_AFFX-r2-Bs-phe_5_signal0.468306
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal733.954590
RawQ3.300282
Spike_AFFX-r2-Bs-lys_5_signal5.599695
Signal(A)15.091743
%A44.059624
Signal(All)133.428329
Corner+Avg:229,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal222.927078
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal2.326158
Spike_AFFX-r2-Ec-bioD_avg-signal663.050415
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P52.547127
Spike_AFFX-r2-Bs-lys_avg-signal5.224974
Spike_AFFX-r2-P1-cre_avg-signal3140.913086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.393249
Spike_AFFX-r2-Bs-thr_3_signal1.497854
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.129249
Spike_AFFX-r2-Bs-dap_3_signal0.889194
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.239482
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal202.145447
#M774
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal8.868694
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.102805
Spike_AFFX-r2-Bs-thr_M_signal9.546921
Signal(P)238.685272
Spike_AFFX-r2-Bs-phe_3-5-ratio2.326158
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10332,Count:9
Spike_AFFX-r2-P1-cre_5_signal3124.742188
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10050
Signal(M)39.982269
BackgroundAvg:85.39,Std:2.87,Min:81.1,Max:93.8
Spike_AFFX-r2-Ec-bioC_avg-signal212.536255
Spike_AFFX-r2-Bs-dap_avg-signal3.220587
Spike_AFFX-r2-Bs-dap_3-5-ratio0.128824
Spike_AFFX-r2-Ec-bioB_5_signal69.808167
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.457951
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-7-bwoll-Ei1_SLD

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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 ("Buchanan-Wollaston_A-7-bwoll-Ein2-1_SRC") 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: Buchanan-Wollaston_A-7-bwoll-Ein2-1_SRC
Organism: Arabidopsis thaliana
Alias: Ein2
Stock Code: N3071
Genetic Background: Columbia
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Genetic Variation: Ein2 transgenic
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.608518
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-ratio1.104374
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.778684
Spike_AFFX-r2-Bs-dap_5_signal1.345789
NoiseAvg:4.26,Std:0.23,Min:3.6,Max:5.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.512687
#P12613
Spike_AFFX-r2-Bs-phe_M_signal1.387315
Corner-Avg:15636,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal72.792412
Spike_AFFX-r2-Ec-bioB_3_signal64.067368
Spike_AFFX-r2-Bs-lys_M_signal7.302609
Spike_AFFX-r2-P1-cre_3_signal3635.759766
Spike_AFFX-r2-Bs-lys_3-5-ratio1.375924
Spike_AFFX-r2-Bs-dap_M_signal4.780956
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.112690
Spike_AFFX-r2-Ec-bioB_avg-signal73.045418
Spike_AFFX-r2-Bs-thr_avg-signal5.472071
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal624.063232
Spike_AFFX-r2-Bs-phe_5_signal10.630676
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal824.375427
RawQ3.031004
Spike_AFFX-r2-Bs-lys_5_signal6.840696
Signal(A)18.878006
%A40.868042
Signal(All)131.722168
Corner+Avg:207,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.600449
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal0.903255
Spike_AFFX-r2-Ec-bioD_avg-signal724.219360
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionM
%P55.295921
Spike_AFFX-r2-Bs-lys_avg-signal7.851862
Spike_AFFX-r2-P1-cre_avg-signal3463.951904
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.836037
Spike_AFFX-r2-Bs-thr_3_signal1.297363
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal4.307082
Spike_AFFX-r2-Bs-dap_3_signal0.632583
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.320981
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal165.443573
#M875
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal9.412281
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.544940
Spike_AFFX-r2-Bs-thr_M_signal3.606161
Signal(P)221.220078
Spike_AFFX-r2-Bs-phe_3-5-ratio0.084967
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:14637,Count:9
Spike_AFFX-r2-P1-cre_5_signal3292.144043
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9322
Signal(M)43.832138
BackgroundAvg:73.93,Std:2.62,Min:67.3,Max:80.7
Spike_AFFX-r2-Ec-bioC_avg-signal210.522003
Spike_AFFX-r2-Bs-dap_avg-signal2.253110
Spike_AFFX-r2-Bs-dap_3-5-ratio0.470046
Spike_AFFX-r2-Ec-bioB_5_signal82.276489
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.608518
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-8-bwoll-Ei2_SLD

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 ("Buchanan-Wollaston_A-8-bwoll-Ein2-2_SRC") 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: Buchanan-Wollaston_A-8-bwoll-Ein2-2_SRC
Organism: Arabidopsis thaliana
Alias: Ein2
Stock Code: N3071
Genetic Background: Columbia
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Genetic Variation: Ein2 transgenic
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.587735
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-ratio1.079599
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.921779
Spike_AFFX-r2-Bs-dap_5_signal7.019546
NoiseAvg:3.39,Std:0.18,Min:2.9,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_signal17.901686
#P11941
Spike_AFFX-r2-Bs-phe_M_signal0.705371
Corner-Avg:12670,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.256950
Spike_AFFX-r2-Ec-bioB_3_signal85.678947
Spike_AFFX-r2-Bs-lys_M_signal4.078352
Spike_AFFX-r2-P1-cre_3_signal4480.483887
Spike_AFFX-r2-Bs-lys_3-5-ratio6.370688
Spike_AFFX-r2-Bs-dap_M_signal0.769376
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.091984
Spike_AFFX-r2-Ec-bioB_avg-signal89.295143
Spike_AFFX-r2-Bs-thr_avg-signal9.607901
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal902.704468
Spike_AFFX-r2-Bs-phe_5_signal2.740320
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1135.593262
RawQ2.658561
Spike_AFFX-r2-Bs-lys_5_signal1.274844
Signal(A)14.868813
%A44.182377
Signal(All)136.327820
Corner+Avg:149,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal334.686310
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal8.686020
Spike_AFFX-r2-Ec-bioD_avg-signal1019.148865
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P52.349846
Spike_AFFX-r2-Bs-lys_avg-signal4.491610
Spike_AFFX-r2-P1-cre_avg-signal4315.310547
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.467777
Spike_AFFX-r2-Bs-thr_3_signal1.646673
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal4.043904
Spike_AFFX-r2-Bs-dap_3_signal2.845574
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.257990
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal277.398773
#M791
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal8.121634
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.206517
Spike_AFFX-r2-Bs-thr_M_signal9.275343
Signal(P)245.393097
Spike_AFFX-r2-Bs-phe_3-5-ratio3.169709
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10824,Count:9
Spike_AFFX-r2-P1-cre_5_signal4150.137207
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10078
Signal(M)37.358810
BackgroundAvg:67.22,Std:2.19,Min:63.1,Max:73.6
Spike_AFFX-r2-Ec-bioC_avg-signal306.042542
Spike_AFFX-r2-Bs-dap_avg-signal3.544832
Spike_AFFX-r2-Bs-dap_3-5-ratio0.405379
Spike_AFFX-r2-Ec-bioB_5_signal92.949539
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.587735
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-9-bwoll-Co1_SLD

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 ("Buchanan-Wollaston_A-9-bwoll-Coi1-1_SRC") 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: Buchanan-Wollaston_A-9-bwoll-Coi1-1_SRC
Organism: Arabidopsis thaliana
Alias: Coi1
Stock Code: N3071
Genetic Background: Columbia
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Genetic Variation: Coi1 transgenic
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.391687
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-ratio1.084236
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.903212
Spike_AFFX-r2-Bs-dap_5_signal5.622534
NoiseAvg:4.87,Std:0.36,Min:4.2,Max:6.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.870657
#P11990
Spike_AFFX-r2-Bs-phe_M_signal1.213532
Corner-Avg:12579,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal49.374512
Spike_AFFX-r2-Ec-bioB_3_signal48.523220
Spike_AFFX-r2-Bs-lys_M_signal5.751832
Spike_AFFX-r2-P1-cre_3_signal2351.513672
Spike_AFFX-r2-Bs-lys_3-5-ratio0.126095
Spike_AFFX-r2-Bs-dap_M_signal1.415965
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.106598
Spike_AFFX-r2-Ec-bioB_avg-signal50.540234
Spike_AFFX-r2-Bs-thr_avg-signal14.767978
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal457.747833
Spike_AFFX-r2-Bs-phe_5_signal6.270160
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal542.670471
RawQ3.188481
Spike_AFFX-r2-Bs-lys_5_signal7.864575
Signal(A)15.759484
%A43.936871
Signal(All)126.762054
Corner+Avg:188,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal176.543549
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal11.088174
Spike_AFFX-r2-Ec-bioD_avg-signal500.209167
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P52.564663
Spike_AFFX-r2-Bs-lys_avg-signal4.869363
Spike_AFFX-r2-P1-cre_avg-signal2260.167725
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.498466
Spike_AFFX-r2-Bs-thr_3_signal2.331376
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal6.190622
Spike_AFFX-r2-Bs-dap_3_signal3.285638
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.185523
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal128.286377
#M798
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal0.991684
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.376168
Spike_AFFX-r2-Bs-thr_M_signal20.101896
Signal(P)225.026840
Spike_AFFX-r2-Bs-phe_3-5-ratio1.768404
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10899,Count:9
Spike_AFFX-r2-P1-cre_5_signal2168.821777
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10022
Signal(M)44.397518
BackgroundAvg:79.44,Std:3.09,Min:72.7,Max:87.0
Spike_AFFX-r2-Ec-bioC_avg-signal152.414963
Spike_AFFX-r2-Bs-dap_avg-signal3.441379
Spike_AFFX-r2-Bs-dap_3-5-ratio0.584370
Spike_AFFX-r2-Ec-bioB_5_signal53.722958
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.391687
NF1.000000
HZ4
Tau0.015000

Slide: Buchanan-Wollaston_A-10-bwoll-Co2_SLD

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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 ("Buchanan-Wollaston_A-10-bwoll-Coi1-2_SRC") 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: Buchanan-Wollaston_A-10-bwoll-Coi1-2_SRC
Organism: Arabidopsis thaliana
Alias: Coi1
Stock Code: N3071
Genetic Background: Columbia
Growth Conditions:
locationGrowth Room
AtmosphereNormal
Humiditynot controlled
Temperature18
Lighting12h day
Mediumcompost
Treatmentnone
Nutrientsnone
Wateras needed
Stratification
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.0
Genetic Variation: Coi1 transgenic
Tissue: fully expanded leaves
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Z6/RNAEasy
Method:
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: 2003-01-23

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:0.600691
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-ratio1.059578
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.427530
Spike_AFFX-r2-Bs-dap_5_signal1.801480
NoiseAvg:3.96,Std:0.19,Min:3.6,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.573681
#P11375
Spike_AFFX-r2-Bs-phe_M_signal1.275678
Corner-Avg:11548,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal106.071129
Spike_AFFX-r2-Ec-bioB_3_signal129.559723
Spike_AFFX-r2-Bs-lys_M_signal0.879924
Spike_AFFX-r2-P1-cre_3_signal4615.460938
Spike_AFFX-r2-Bs-lys_3-5-ratio3.689101
Spike_AFFX-r2-Bs-dap_M_signal4.877668
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.092149
Spike_AFFX-r2-Ec-bioB_avg-signal108.796272
Spike_AFFX-r2-Bs-thr_avg-signal16.041388
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal1005.182983
Spike_AFFX-r2-Bs-phe_5_signal3.904330
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1171.863159
RawQ2.981405
Spike_AFFX-r2-Bs-lys_5_signal2.376629
Signal(A)16.322615
%A46.742657
Signal(All)135.280304
Corner+Avg:164,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal332.741791
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal8.218129
Spike_AFFX-r2-Ec-bioD_avg-signal1088.523071
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P49.868477
Spike_AFFX-r2-Bs-lys_avg-signal4.008059
Spike_AFFX-r2-P1-cre_avg-signal4485.701172
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.388865
Spike_AFFX-r2-Bs-thr_3_signal1.803691
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal4.466046
Spike_AFFX-r2-Bs-dap_3_signal0.717488
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.165821
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal319.265900
#M773
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal8.767624
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.042209
Spike_AFFX-r2-Bs-thr_M_signal26.746786
Signal(P)252.953278
Spike_AFFX-r2-Bs-phe_3-5-ratio2.104875
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10880,Count:9
Spike_AFFX-r2-P1-cre_5_signal4355.940918
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10662
Signal(M)44.461014
BackgroundAvg:75.78,Std:2.49,Min:71.3,Max:82.5
Spike_AFFX-r2-Ec-bioC_avg-signal326.003845
Spike_AFFX-r2-Bs-dap_avg-signal2.465545
Spike_AFFX-r2-Bs-dap_3-5-ratio0.398277
Spike_AFFX-r2-Ec-bioB_5_signal90.757957
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.600691
NF1.000000
HZ4
Tau0.015000


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