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Experiment: abi4 x vtc2

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-542

We crossed the Arabidopsis low vitamin C mutant, vtc2, which has about 25% of wild-type ascorbic acid, and the abscisic acid (ABA) insensitive mutant, abi4.The aim of this work is investigate the cross talk between the abcisic acid and ascorbic acid pathways. Plants were grown for 6 weeks at 22ºC under low (250 µmol m-2 s-1) light with a 10-h photoperiod and 70% humidity.

About the Experimenter

Name:Dr Pedro Diaz
Head of Lab Name:Prof Christine Foyer
Lab:
Address:Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds
Leeds, West Yorkshire, LS2 9JT, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 44(0) 113 34 31415

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
Number of Slides:20
 
Experimental Parameters:
parametergenetic_variation
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Diaz: abi4 x vtc2

Slide: Diaz_542-1_abi4_12-wks_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 ("Diaz_542-1_abi4_12-wks_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: Diaz_542-1_abi4_12-wks_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: abscisic acid insensitive
Stock Code: N3836
Genetic Background: Col, gl1-1 (Columbia)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.817338
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-ratio1.177367
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.861135
Spike_AFFX-r2-Bs-dap_5_signal121.075386
NoiseAvg:2.27,Std:0.08,Min:2.0,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal68.667068
#P13625
Spike_AFFX-r2-Bs-phe_M_signal60.567989
Corner-Avg:5739,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.986641
Spike_AFFX-r2-Ec-bioB_3_signal59.435757
Spike_AFFX-r2-Bs-lys_M_signal29.792051
Spike_AFFX-r2-P1-cre_3_signal4929.559570
Spike_AFFX-r2-Bs-lys_3-5-ratio2.149999
Spike_AFFX-r2-Bs-dap_M_signal281.723938
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.867119
Spike_AFFX-r2-Ec-bioB_avg-signal73.814209
Spike_AFFX-r2-Bs-thr_avg-signal161.958984
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal824.032532
Spike_AFFX-r2-Bs-phe_5_signal74.965126
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1403.928101
RawQ2.179824
Spike_AFFX-r2-Bs-lys_5_signal38.428936
Signal(A)5.128699
%A38.548882
Signal(All)151.666077
Corner+Avg:71,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal345.665070
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal69.872086
Spike_AFFX-r2-Ec-bioD_avg-signal1113.980347
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.732574
Spike_AFFX-r2-Bs-lys_avg-signal50.281052
Spike_AFFX-r2-P1-cre_avg-signal4558.247070
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.718544
Spike_AFFX-r2-Bs-thr_3_signal265.543701
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-signal68.468407
Spike_AFFX-r2-Bs-dap_3_signal359.901337
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.703729
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal323.638916
#M392
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.622162
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.068058
Spike_AFFX-r2-Bs-thr_M_signal151.666199
Signal(P)250.034225
Spike_AFFX-r2-Bs-phe_3-5-ratio0.932061
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4252,Count:9
Spike_AFFX-r2-P1-cre_5_signal4186.935059
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8793
Signal(M)19.618366
BackgroundAvg:77.93,Std:0.37,Min:76.6,Max:78.8
Spike_AFFX-r2-Ec-bioC_avg-signal334.651978
Spike_AFFX-r2-Bs-dap_avg-signal254.233536
Spike_AFFX-r2-Bs-dap_3-5-ratio2.972539
Spike_AFFX-r2-Ec-bioB_5_signal69.020233
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.817338
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-2_abi4_12-wks_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 ("Diaz_542-2_abi4_12-wks_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: Diaz_542-2_abi4_12-wks_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: abscisic acid insensitive
Stock Code: N3836
Genetic Background: Col, gl1-1 (Columbia)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.58397
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-ratio1.133369
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.850517
Spike_AFFX-r2-Bs-dap_5_signal57.013004
NoiseAvg:2.56,Std:0.08,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal38.624870
#P13685
Spike_AFFX-r2-Bs-phe_M_signal42.219681
Corner-Avg:7492,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.658127
Spike_AFFX-r2-Ec-bioB_3_signal68.304840
Spike_AFFX-r2-Bs-lys_M_signal16.605156
Spike_AFFX-r2-P1-cre_3_signal4319.093750
Spike_AFFX-r2-Bs-lys_3-5-ratio1.852729
Spike_AFFX-r2-Bs-dap_M_signal192.237213
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.803860
Spike_AFFX-r2-Ec-bioB_avg-signal81.757576
Spike_AFFX-r2-Bs-thr_avg-signal76.439056
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal848.940430
Spike_AFFX-r2-Bs-phe_5_signal48.889091
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1402.553223
RawQ2.375135
Spike_AFFX-r2-Bs-lys_5_signal23.908089
Signal(A)4.388033
%A38.373520
Signal(All)152.627838
Corner+Avg:85,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal318.232574
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal54.402760
Spike_AFFX-r2-Ec-bioD_avg-signal1125.746826
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.995617
Spike_AFFX-r2-Bs-lys_avg-signal28.269484
Spike_AFFX-r2-P1-cre_avg-signal4064.969727
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.630864
Spike_AFFX-r2-Bs-thr_3_signal108.298737
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.503845
Spike_AFFX-r2-Bs-dap_3_signal226.439880
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.652122
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal305.861847
#M372
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.295204
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.040445
Spike_AFFX-r2-Bs-thr_M_signal82.393555
Signal(P)251.123230
Spike_AFFX-r2-Bs-phe_3-5-ratio1.112779
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6081,Count:9
Spike_AFFX-r2-P1-cre_5_signal3810.845947
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8753
Signal(M)17.234335
BackgroundAvg:85.26,Std:0.46,Min:84.0,Max:86.6
Spike_AFFX-r2-Ec-bioC_avg-signal312.047211
Spike_AFFX-r2-Bs-dap_avg-signal158.563370
Spike_AFFX-r2-Bs-dap_3-5-ratio3.971723
Spike_AFFX-r2-Ec-bioB_5_signal80.309753
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.583970
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-3_abi4_12-wks_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 ("Diaz_542-3_abi4_12-wks_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: Diaz_542-3_abi4_12-wks_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: abscisic acid insensitive
Stock Code: N3836
Genetic Background: Col, gl1-1 (Columbia)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.577903
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-ratio1.369117
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.054139
Spike_AFFX-r2-Bs-dap_5_signal86.817795
NoiseAvg:2.54,Std:0.05,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal47.039810
#P14223
Spike_AFFX-r2-Bs-phe_M_signal47.342133
Corner-Avg:7144,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.772552
Spike_AFFX-r2-Ec-bioB_3_signal56.856979
Spike_AFFX-r2-Bs-lys_M_signal13.425392
Spike_AFFX-r2-P1-cre_3_signal4401.907715
Spike_AFFX-r2-Bs-lys_3-5-ratio1.954191
Spike_AFFX-r2-Bs-dap_M_signal214.081833
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.376283
Spike_AFFX-r2-Ec-bioB_avg-signal64.855476
Spike_AFFX-r2-Bs-thr_avg-signal85.502708
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal816.694946
Spike_AFFX-r2-Bs-phe_5_signal48.896648
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1302.529297
RawQ2.334626
Spike_AFFX-r2-Bs-lys_5_signal24.704905
Signal(A)3.981816
%A36.014904
Signal(All)147.159103
Corner+Avg:81,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal274.450409
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal51.210934
Spike_AFFX-r2-Ec-bioD_avg-signal1059.612061
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.354229
Spike_AFFX-r2-Bs-lys_avg-signal28.802797
Spike_AFFX-r2-P1-cre_avg-signal3808.525391
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.630864
Spike_AFFX-r2-Bs-thr_3_signal111.779915
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal49.149906
Spike_AFFX-r2-Bs-dap_3_signal235.537521
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.594879
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.474960
#M372
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.278095
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.118038
Spike_AFFX-r2-Bs-thr_M_signal97.688370
Signal(P)233.286224
Spike_AFFX-r2-Bs-phe_3-5-ratio1.047330
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5179,Count:9
Spike_AFFX-r2-P1-cre_5_signal3215.142822
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8215
Signal(M)16.017294
BackgroundAvg:82.45,Std:1.26,Min:78.9,Max:85.5
Spike_AFFX-r2-Ec-bioC_avg-signal259.962677
Spike_AFFX-r2-Bs-dap_avg-signal178.812378
Spike_AFFX-r2-Bs-dap_3-5-ratio2.713010
Spike_AFFX-r2-Ec-bioB_5_signal53.936893
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.577903
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-4_abi4_12-wks_Rep4_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Diaz_542-4_abi4_12-wks_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Diaz_542-4_abi4_12-wks_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: abscisic acid insensitive
Stock Code: N3836
Genetic Background: Col, gl1-1 (Columbia)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.60559
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-ratio1.418658
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.178696
Spike_AFFX-r2-Bs-dap_5_signal101.989662
NoiseAvg:2.33,Std:0.08,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal48.927036
#P14040
Spike_AFFX-r2-Bs-phe_M_signal65.234200
Corner-Avg:7443,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.893486
Spike_AFFX-r2-Ec-bioB_3_signal67.757530
Spike_AFFX-r2-Bs-lys_M_signal19.409370
Spike_AFFX-r2-P1-cre_3_signal5277.236816
Spike_AFFX-r2-Bs-lys_3-5-ratio1.213023
Spike_AFFX-r2-Bs-dap_M_signal253.864487
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.768354
Spike_AFFX-r2-Ec-bioB_avg-signal70.712059
Spike_AFFX-r2-Bs-thr_avg-signal114.209633
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal926.668213
Spike_AFFX-r2-Bs-phe_5_signal82.615585
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1323.967529
RawQ2.060917
Spike_AFFX-r2-Bs-lys_5_signal40.885185
Signal(A)4.316827
%A36.567295
Signal(All)149.864746
Corner+Avg:94,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal276.919708
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal84.575142
Spike_AFFX-r2-Ec-bioD_avg-signal1125.317871
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.551952
Spike_AFFX-r2-Bs-lys_avg-signal36.629749
Spike_AFFX-r2-P1-cre_avg-signal4498.557617
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.880754
Spike_AFFX-r2-Bs-thr_3_signal184.374405
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-signal77.474976
Spike_AFFX-r2-Bs-dap_3_signal373.466949
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.428740
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal278.545776
#M429
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.594688
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.994162
Spike_AFFX-r2-Bs-thr_M_signal109.327469
Signal(P)240.409103
Spike_AFFX-r2-Bs-phe_3-5-ratio1.023719
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5083,Count:9
Spike_AFFX-r2-P1-cre_5_signal3719.878418
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8341
Signal(M)16.467197
BackgroundAvg:51.01,Std:0.75,Min:49.8,Max:53.2
Spike_AFFX-r2-Ec-bioC_avg-signal277.732727
Spike_AFFX-r2-Bs-dap_avg-signal243.107040
Spike_AFFX-r2-Bs-dap_3-5-ratio3.661812
Spike_AFFX-r2-Ec-bioB_5_signal57.485146
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.605590
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-5_vtc2_5_12-wks_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Diaz_542-5_vtc2_5_12-wks_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: Diaz_542-5_vtc2_5_12-wks_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_076245 (AO) (CG)
Stock Code: N576245
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: T-DNA insertion
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.478366
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-ratio1.415850
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.237817
Spike_AFFX-r2-Bs-dap_5_signal39.202065
NoiseAvg:2.93,Std:0.09,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.726685
#P14375
Spike_AFFX-r2-Bs-phe_M_signal26.788063
Corner-Avg:7597,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal59.157513
Spike_AFFX-r2-Ec-bioB_3_signal54.154667
Spike_AFFX-r2-Bs-lys_M_signal13.484871
Spike_AFFX-r2-P1-cre_3_signal3551.561279
Spike_AFFX-r2-Bs-lys_3-5-ratio1.773177
Spike_AFFX-r2-Bs-dap_M_signal85.393242
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.258026
Spike_AFFX-r2-Ec-bioB_avg-signal52.354107
Spike_AFFX-r2-Bs-thr_avg-signal43.544758
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal575.156250
Spike_AFFX-r2-Bs-phe_5_signal16.756186
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal851.878174
RawQ2.465117
Spike_AFFX-r2-Bs-lys_5_signal12.299326
Signal(A)3.904054
%A35.339764
Signal(All)143.395874
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal203.794785
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.672720
Spike_AFFX-r2-Ec-bioD_avg-signal713.517212
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.020603
Spike_AFFX-r2-Bs-lys_avg-signal15.864360
Spike_AFFX-r2-P1-cre_avg-signal3029.995605
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.639632
Spike_AFFX-r2-Bs-thr_3_signal67.528076
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-signal23.738991
Spike_AFFX-r2-Bs-dap_3_signal150.453415
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.481125
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal155.139725
#M374
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.808886
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.313621
Spike_AFFX-r2-Bs-thr_M_signal42.379520
Signal(P)224.930786
Spike_AFFX-r2-Bs-phe_3-5-ratio1.651493
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4803,Count:9
Spike_AFFX-r2-P1-cre_5_signal2508.429688
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8061
Signal(M)16.068129
BackgroundAvg:64.68,Std:1.20,Min:62.3,Max:68.2
Spike_AFFX-r2-Ec-bioC_avg-signal179.467255
Spike_AFFX-r2-Bs-dap_avg-signal91.682899
Spike_AFFX-r2-Bs-dap_3-5-ratio3.837895
Spike_AFFX-r2-Ec-bioB_5_signal43.750141
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.478366
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-6_vtc2_7_12-wks_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 ("Diaz_542-6_vtc2_7_12-wks_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: Diaz_542-6_vtc2_7_12-wks_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_076245 (AO) (CG)
Stock Code: N576245
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: T-DNA insertion
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.667994
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-ratio1.434932
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.765988
Spike_AFFX-r2-Bs-dap_5_signal87.579094
NoiseAvg:2.40,Std:0.09,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal45.565231
#P14088
Spike_AFFX-r2-Bs-phe_M_signal50.571495
Corner-Avg:6655,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal78.610306
Spike_AFFX-r2-Ec-bioB_3_signal40.958069
Spike_AFFX-r2-Bs-lys_M_signal14.922249
Spike_AFFX-r2-P1-cre_3_signal4844.266602
Spike_AFFX-r2-Bs-lys_3-5-ratio2.471528
Spike_AFFX-r2-Bs-dap_M_signal208.562790
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.315938
Spike_AFFX-r2-Ec-bioB_avg-signal57.679760
Spike_AFFX-r2-Bs-thr_avg-signal96.510963
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal746.969055
Spike_AFFX-r2-Bs-phe_5_signal53.688084
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1195.273804
RawQ2.126668
Spike_AFFX-r2-Bs-lys_5_signal25.534046
Signal(A)4.355499
%A36.343708
Signal(All)148.617020
Corner+Avg:87,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal248.686127
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.673603
Spike_AFFX-r2-Ec-bioD_avg-signal971.121460
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.762386
Spike_AFFX-r2-Bs-lys_avg-signal34.521465
Spike_AFFX-r2-P1-cre_avg-signal4110.111816
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.893906
Spike_AFFX-r2-Bs-thr_3_signal151.091507
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-signal55.311062
Spike_AFFX-r2-Bs-dap_3_signal266.416534
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.600165
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal251.518478
#M432
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal63.108105
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.988739
Spike_AFFX-r2-Bs-thr_M_signal92.876175
Signal(P)237.539185
Spike_AFFX-r2-Bs-phe_3-5-ratio1.148739
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4157,Count:9
Spike_AFFX-r2-P1-cre_5_signal3375.956787
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8290
Signal(M)17.118702
BackgroundAvg:55.07,Std:0.83,Min:53.7,Max:57.3
Spike_AFFX-r2-Ec-bioC_avg-signal250.102295
Spike_AFFX-r2-Bs-dap_avg-signal187.519470
Spike_AFFX-r2-Bs-dap_3-5-ratio3.042011
Spike_AFFX-r2-Ec-bioB_5_signal53.470901
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.667994
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-7_vtc2_8_12-wks_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Diaz_542-7_vtc2_8_12-wks_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: Diaz_542-7_vtc2_8_12-wks_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_076245 (AO) (CG)
Stock Code: N576245
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: T-DNA insertion
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.591822
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-ratio1.359059
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.973216
Spike_AFFX-r2-Bs-dap_5_signal97.243515
NoiseAvg:2.64,Std:0.09,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal51.855301
#P14307
Spike_AFFX-r2-Bs-phe_M_signal46.668312
Corner-Avg:7611,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.000198
Spike_AFFX-r2-Ec-bioB_3_signal49.673206
Spike_AFFX-r2-Bs-lys_M_signal15.327961
Spike_AFFX-r2-P1-cre_3_signal4392.466797
Spike_AFFX-r2-Bs-lys_3-5-ratio1.232818
Spike_AFFX-r2-Bs-dap_M_signal235.356644
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.100444
Spike_AFFX-r2-Ec-bioB_avg-signal61.571217
Spike_AFFX-r2-Bs-thr_avg-signal102.205635
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal670.191895
Spike_AFFX-r2-Bs-phe_5_signal58.926510
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1018.730896
RawQ2.403958
Spike_AFFX-r2-Bs-lys_5_signal29.986656
Signal(A)4.284457
%A35.637878
Signal(All)143.925629
Corner+Avg:97,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal230.128235
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.657135
Spike_AFFX-r2-Ec-bioD_avg-signal844.461426
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.722488
Spike_AFFX-r2-Bs-lys_avg-signal27.427572
Spike_AFFX-r2-P1-cre_avg-signal3812.229248
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.639632
Spike_AFFX-r2-Bs-thr_3_signal160.774460
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-signal55.750652
Spike_AFFX-r2-Bs-dap_3_signal238.808823
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.520059
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal240.960968
#M374
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.968094
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.955044
Spike_AFFX-r2-Bs-thr_M_signal93.987152
Signal(P)226.619263
Spike_AFFX-r2-Bs-phe_3-5-ratio1.046340
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5705,Count:9
Spike_AFFX-r2-P1-cre_5_signal3231.991699
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8129
Signal(M)15.704304
BackgroundAvg:60.24,Std:0.71,Min:58.2,Max:61.9
Spike_AFFX-r2-Ec-bioC_avg-signal235.544601
Spike_AFFX-r2-Bs-dap_avg-signal190.469666
Spike_AFFX-r2-Bs-dap_3-5-ratio2.455781
Spike_AFFX-r2-Ec-bioB_5_signal51.040245
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.591822
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-8_vtc2_9_12-wks_Rep4_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Diaz_542-8_vtc2_9_12-wks_Rep4_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Diaz_542-8_vtc2_9_12-wks_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_076245 (AO) (CG)
Stock Code: N576245
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: T-DNA insertion
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.637115
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-ratio1.416390
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.742003
Spike_AFFX-r2-Bs-dap_5_signal93.765114
NoiseAvg:2.37,Std:0.08,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal41.269459
#P14298
Spike_AFFX-r2-Bs-phe_M_signal62.028812
Corner-Avg:7158,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal73.684525
Spike_AFFX-r2-Ec-bioB_3_signal52.168442
Spike_AFFX-r2-Bs-lys_M_signal22.390329
Spike_AFFX-r2-P1-cre_3_signal4749.000488
Spike_AFFX-r2-Bs-lys_3-5-ratio1.605152
Spike_AFFX-r2-Bs-dap_M_signal230.562790
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.043107
Spike_AFFX-r2-Ec-bioB_avg-signal65.386848
Spike_AFFX-r2-Bs-thr_avg-signal94.868568
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal744.525269
Spike_AFFX-r2-Bs-phe_5_signal86.929253
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1136.797363
RawQ2.130004
Spike_AFFX-r2-Bs-lys_5_signal31.029459
Signal(A)4.096840
%A35.874615
Signal(All)145.754028
Corner+Avg:93,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal236.586746
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal54.566746
Spike_AFFX-r2-Ec-bioD_avg-signal940.661316
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.683033
Spike_AFFX-r2-Bs-lys_avg-signal34.408932
Spike_AFFX-r2-P1-cre_avg-signal4050.945801
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.442350
Spike_AFFX-r2-Bs-thr_3_signal125.587379
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal67.841606
Spike_AFFX-r2-Bs-dap_3_signal323.981842
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.526875
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.017609
#M329
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.807007
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.989830
Spike_AFFX-r2-Bs-thr_M_signal117.748856
Signal(P)229.786697
Spike_AFFX-r2-Bs-phe_3-5-ratio0.627714
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4802,Count:9
Spike_AFFX-r2-P1-cre_5_signal3352.891113
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8183
Signal(M)17.126722
BackgroundAvg:54.78,Std:0.54,Min:53.6,Max:55.9
Spike_AFFX-r2-Ec-bioC_avg-signal237.802185
Spike_AFFX-r2-Bs-dap_avg-signal216.103256
Spike_AFFX-r2-Bs-dap_3-5-ratio3.455249
Spike_AFFX-r2-Ec-bioB_5_signal70.307587
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.637115
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-9_xL1_14_12-wks_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Diaz_542-9_xL1_14_12-wks_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: Diaz_542-9_xL1_14_12-wks_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.710241
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-ratio1.304547
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.799593
Spike_AFFX-r2-Bs-dap_5_signal87.548409
NoiseAvg:2.35,Std:0.04,Min:2.2,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal58.208538
#P14002
Spike_AFFX-r2-Bs-phe_M_signal62.095318
Corner-Avg:7479,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal103.239616
Spike_AFFX-r2-Ec-bioB_3_signal75.901817
Spike_AFFX-r2-Bs-lys_M_signal18.991989
Spike_AFFX-r2-P1-cre_3_signal5167.154297
Spike_AFFX-r2-Bs-lys_3-5-ratio1.486599
Spike_AFFX-r2-Bs-dap_M_signal231.232086
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.615671
Spike_AFFX-r2-Ec-bioB_avg-signal91.355652
Spike_AFFX-r2-Bs-thr_avg-signal105.500130
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal960.780945
Spike_AFFX-r2-Bs-phe_5_signal67.384460
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1355.922119
RawQ2.294928
Spike_AFFX-r2-Bs-lys_5_signal41.464787
Signal(A)4.461398
%A37.036388
Signal(All)147.772171
Corner+Avg:115,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal333.574310
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal71.991714
Spike_AFFX-r2-Ec-bioD_avg-signal1158.351563
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.385357
Spike_AFFX-r2-Bs-lys_avg-signal40.699432
Spike_AFFX-r2-P1-cre_avg-signal4564.017578
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal152.254410
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal67.157166
Spike_AFFX-r2-Bs-dap_3_signal306.432404
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.411271
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal287.635559
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.641521
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.159712
Spike_AFFX-r2-Bs-thr_M_signal106.037445
Signal(P)237.576309
Spike_AFFX-r2-Bs-phe_3-5-ratio1.068373
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6313,Count:9
Spike_AFFX-r2-P1-cre_5_signal3960.880615
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8448
Signal(M)17.916216
BackgroundAvg:56.69,Std:0.43,Min:55.6,Max:57.8
Spike_AFFX-r2-Ec-bioC_avg-signal310.604919
Spike_AFFX-r2-Bs-dap_avg-signal208.404297
Spike_AFFX-r2-Bs-dap_3-5-ratio3.500148
Spike_AFFX-r2-Ec-bioB_5_signal94.925514
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.710241
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-10_xL1_16_12-wks_Rep2_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 ("Diaz_542-10_xL1_16_12-wks_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: Diaz_542-10_xL1_16_12-wks_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.557481
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-ratio1.287629
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.897324
Spike_AFFX-r2-Bs-dap_5_signal49.532978
NoiseAvg:2.80,Std:0.09,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal34.713783
#P14120
Spike_AFFX-r2-Bs-phe_M_signal33.873272
Corner-Avg:7573,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.580170
Spike_AFFX-r2-Ec-bioB_3_signal51.284271
Spike_AFFX-r2-Bs-lys_M_signal12.974905
Spike_AFFX-r2-P1-cre_3_signal4336.548340
Spike_AFFX-r2-Bs-lys_3-5-ratio1.315106
Spike_AFFX-r2-Bs-dap_M_signal135.666412
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.230787
Spike_AFFX-r2-Ec-bioB_avg-signal64.672310
Spike_AFFX-r2-Bs-thr_avg-signal61.787769
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal773.880554
Spike_AFFX-r2-Bs-phe_5_signal47.788521
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1164.126099
RawQ2.478925
Spike_AFFX-r2-Bs-lys_5_signal18.319220
Signal(A)4.504974
%A36.317406
Signal(All)145.121567
Corner+Avg:92,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal282.371124
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.256931
Spike_AFFX-r2-Ec-bioD_avg-signal969.003296
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.902676
Spike_AFFX-r2-Bs-lys_avg-signal18.461945
Spike_AFFX-r2-P1-cre_avg-signal3852.202393
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.779921
Spike_AFFX-r2-Bs-thr_3_signal77.439056
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal40.306240
Spike_AFFX-r2-Bs-dap_3_signal176.369873
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.504271
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal270.599792
#M406
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.091711
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.043501
Spike_AFFX-r2-Bs-thr_M_signal73.210472
Signal(P)231.295517
Spike_AFFX-r2-Bs-phe_3-5-ratio0.821472
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6267,Count:9
Spike_AFFX-r2-P1-cre_5_signal3367.856445
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8284
Signal(M)17.268030
BackgroundAvg:64.14,Std:0.49,Min:62.7,Max:65.4
Spike_AFFX-r2-Ec-bioC_avg-signal276.485474
Spike_AFFX-r2-Bs-dap_avg-signal120.523094
Spike_AFFX-r2-Bs-dap_3-5-ratio3.560656
Spike_AFFX-r2-Ec-bioB_5_signal57.152477
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.557481
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-11_xL1_17_12-wks_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 ("Diaz_542-11_xL1_17_12-wks_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: Diaz_542-11_xL1_17_12-wks_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.525856
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-ratio1.177557
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.038941
Spike_AFFX-r2-Bs-dap_5_signal0.760772
NoiseAvg:2.92,Std:0.05,Min:2.8,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal0.231363
#P14214
Spike_AFFX-r2-Bs-phe_M_signal0.868874
Corner-Avg:7906,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal73.730293
Spike_AFFX-r2-Ec-bioB_3_signal50.134586
Spike_AFFX-r2-Bs-lys_M_signal0.314100
Spike_AFFX-r2-P1-cre_3_signal3202.336182
Spike_AFFX-r2-Bs-lys_3-5-ratio3.108944
Spike_AFFX-r2-Bs-dap_M_signal0.275900
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.329726
Spike_AFFX-r2-Ec-bioB_avg-signal57.373447
Spike_AFFX-r2-Bs-thr_avg-signal3.314260
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal535.067444
Spike_AFFX-r2-Bs-phe_5_signal5.505539
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1061.001953
RawQ2.630456
Spike_AFFX-r2-Bs-lys_5_signal2.610412
Signal(A)4.184918
%A36.032440
Signal(All)143.265793
Corner+Avg:95,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal233.092941
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal4.628533
Spike_AFFX-r2-Ec-bioD_avg-signal798.034668
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P62.314774
Spike_AFFX-r2-Bs-lys_avg-signal3.680046
Spike_AFFX-r2-P1-cre_avg-signal2960.905273
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.652784
Spike_AFFX-r2-Bs-thr_3_signal0.329726
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-signal3.667649
Spike_AFFX-r2-Bs-dap_3_signal0.329451
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.982931
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.235809
#M377
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal8.115625
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.974323
Spike_AFFX-r2-Bs-thr_M_signal9.381692
Signal(P)227.024048
Spike_AFFX-r2-Bs-phe_3-5-ratio0.840705
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:6124,Count:9
Spike_AFFX-r2-P1-cre_5_signal2719.474365
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8219
Signal(M)17.446241
BackgroundAvg:65.95,Std:0.46,Min:64.5,Max:67.2
Spike_AFFX-r2-Ec-bioC_avg-signal236.164368
Spike_AFFX-r2-Bs-dap_avg-signal0.455374
Spike_AFFX-r2-Bs-dap_3-5-ratio0.329451
Spike_AFFX-r2-Ec-bioB_5_signal48.255466
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.525856
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-12_X-12_12-wks_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Diaz_542-12_X-12_12-wks_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: Diaz_542-12_X-12_12-wks_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:1.081244
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-ratio1.359422
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.628518
Spike_AFFX-r2-Bs-dap_5_signal94.379707
NoiseAvg:2.07,Std:0.04,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal49.360878
#P13751
Spike_AFFX-r2-Bs-phe_M_signal48.252243
Corner-Avg:6056,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal97.448456
Spike_AFFX-r2-Ec-bioB_3_signal48.106266
Spike_AFFX-r2-Bs-lys_M_signal16.426918
Spike_AFFX-r2-P1-cre_3_signal5922.866211
Spike_AFFX-r2-Bs-lys_3-5-ratio0.833948
Spike_AFFX-r2-Bs-dap_M_signal152.191849
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.676186
Spike_AFFX-r2-Ec-bioB_avg-signal74.031303
Spike_AFFX-r2-Bs-thr_avg-signal75.340660
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal864.198303
Spike_AFFX-r2-Bs-phe_5_signal50.571415
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1409.993408
RawQ2.142780
Spike_AFFX-r2-Bs-lys_5_signal28.715954
Signal(A)5.038765
%A37.943886
Signal(All)152.302856
Corner+Avg:70,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal288.165436
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.317402
Spike_AFFX-r2-Ec-bioD_avg-signal1137.095825
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.284962
Spike_AFFX-r2-Bs-lys_avg-signal23.030161
Spike_AFFX-r2-P1-cre_avg-signal5139.883789
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.771153
Spike_AFFX-r2-Bs-thr_3_signal82.738007
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal43.713684
Spike_AFFX-r2-Bs-dap_3_signal233.846298
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.631562
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal252.278320
#M404
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.947615
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.142252
Spike_AFFX-r2-Bs-thr_M_signal93.923103
Signal(P)248.900146
Spike_AFFX-r2-Bs-phe_3-5-ratio0.639045
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4490,Count:9
Spike_AFFX-r2-P1-cre_5_signal4356.900879
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8655
Signal(M)19.286474
BackgroundAvg:52.45,Std:0.50,Min:51.2,Max:53.9
Spike_AFFX-r2-Ec-bioC_avg-signal270.221863
Spike_AFFX-r2-Bs-dap_avg-signal160.139282
Spike_AFFX-r2-Bs-dap_3-5-ratio2.477718
Spike_AFFX-r2-Ec-bioB_5_signal76.539192
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.081244
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-13_X-12_12-wks_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 ("Diaz_542-13_X-12_12-wks_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: Diaz_542-13_X-12_12-wks_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.873714
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-ratio1.251641
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.721890
Spike_AFFX-r2-Bs-dap_5_signal110.698639
NoiseAvg:2.08,Std:0.05,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal52.709072
#P13861
Spike_AFFX-r2-Bs-phe_M_signal38.489193
Corner-Avg:5768,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal94.859070
Spike_AFFX-r2-Ec-bioB_3_signal65.726471
Spike_AFFX-r2-Bs-lys_M_signal18.302805
Spike_AFFX-r2-P1-cre_3_signal5462.776855
Spike_AFFX-r2-Bs-lys_3-5-ratio1.565319
Spike_AFFX-r2-Bs-dap_M_signal224.537720
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.258539
Spike_AFFX-r2-Ec-bioB_avg-signal83.877769
Spike_AFFX-r2-Bs-thr_avg-signal95.706947
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal946.442993
Spike_AFFX-r2-Bs-phe_5_signal50.891716
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1517.360962
RawQ2.110840
Spike_AFFX-r2-Bs-lys_5_signal29.818293
Signal(A)4.905869
%A37.553703
Signal(All)147.550690
Corner+Avg:67,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal407.567932
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal48.085812
Spike_AFFX-r2-Ec-bioD_avg-signal1231.901978
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.767208
Spike_AFFX-r2-Bs-lys_avg-signal31.598742
Spike_AFFX-r2-P1-cre_avg-signal4913.633789
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.679088
Spike_AFFX-r2-Bs-thr_3_signal119.045494
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal45.822239
Spike_AFFX-r2-Bs-dap_3_signal286.202728
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.603225
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal291.915985
#M383
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.675129
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.396182
Spike_AFFX-r2-Bs-thr_M_signal115.366280
Signal(P)239.248520
Spike_AFFX-r2-Bs-phe_3-5-ratio0.944865
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5137,Count:9
Spike_AFFX-r2-P1-cre_5_signal4364.491211
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8566
Signal(M)19.278753
BackgroundAvg:73.04,Std:0.18,Min:72.5,Max:73.6
Spike_AFFX-r2-Ec-bioC_avg-signal349.741943
Spike_AFFX-r2-Bs-dap_avg-signal207.146362
Spike_AFFX-r2-Bs-dap_3-5-ratio2.585422
Spike_AFFX-r2-Ec-bioB_5_signal91.047768
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.873714
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-14_X-12_12-wks_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 ("Diaz_542-14_X-12_12-wks_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: Diaz_542-14_X-12_12-wks_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.712448
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-ratio1.284399
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.949958
Spike_AFFX-r2-Bs-dap_5_signal78.341377
NoiseAvg:2.35,Std:0.06,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal40.826057
#P13989
Spike_AFFX-r2-Bs-phe_M_signal41.156757
Corner-Avg:6882,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.755165
Spike_AFFX-r2-Ec-bioB_3_signal59.206387
Spike_AFFX-r2-Bs-lys_M_signal17.715786
Spike_AFFX-r2-P1-cre_3_signal4303.575195
Spike_AFFX-r2-Bs-lys_3-5-ratio1.307891
Spike_AFFX-r2-Bs-dap_M_signal143.597305
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.298144
Spike_AFFX-r2-Ec-bioB_avg-signal68.428932
Spike_AFFX-r2-Bs-thr_avg-signal71.586143
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal674.043701
Spike_AFFX-r2-Bs-phe_5_signal37.400642
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1162.103638
RawQ2.264429
Spike_AFFX-r2-Bs-lys_5_signal18.277018
Signal(A)3.878354
%A36.996933
Signal(All)145.373947
Corner+Avg:81,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.688721
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.630276
Spike_AFFX-r2-Ec-bioD_avg-signal918.073669
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.328365
Spike_AFFX-r2-Bs-lys_avg-signal19.965715
Spike_AFFX-r2-P1-cre_avg-signal3827.113770
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.674704
Spike_AFFX-r2-Bs-thr_3_signal93.824173
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-signal41.729225
Spike_AFFX-r2-Bs-dap_3_signal203.053711
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.724078
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal281.329376
#M382
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.904346
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.908859
Spike_AFFX-r2-Bs-thr_M_signal80.108208
Signal(P)234.235809
Spike_AFFX-r2-Bs-phe_3-5-ratio1.246777
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5618,Count:9
Spike_AFFX-r2-P1-cre_5_signal3350.652588
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8439
Signal(M)17.082296
BackgroundAvg:78.18,Std:0.34,Min:77.2,Max:79.0
Spike_AFFX-r2-Ec-bioC_avg-signal268.509033
Spike_AFFX-r2-Bs-dap_avg-signal141.664124
Spike_AFFX-r2-Bs-dap_3-5-ratio2.591909
Spike_AFFX-r2-Ec-bioB_5_signal62.325264
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.712448
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-15_x_13_6-wks_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Diaz_542-15_x_13_6-wks_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: Diaz_542-15_x_13_6-wks_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 6 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.818276
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-ratio1.201200
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.069131
Spike_AFFX-r2-Bs-dap_5_signal82.731735
NoiseAvg:2.47,Std:0.08,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal52.260555
#P13656
Spike_AFFX-r2-Bs-phe_M_signal48.776573
Corner-Avg:6626,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal87.173248
Spike_AFFX-r2-Ec-bioB_3_signal62.197411
Spike_AFFX-r2-Bs-lys_M_signal16.122473
Spike_AFFX-r2-P1-cre_3_signal3973.205078
Spike_AFFX-r2-Bs-lys_3-5-ratio1.322350
Spike_AFFX-r2-Bs-dap_M_signal180.178452
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.093455
Spike_AFFX-r2-Ec-bioB_avg-signal69.182106
Spike_AFFX-r2-Bs-thr_avg-signal90.862984
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal662.093018
Spike_AFFX-r2-Bs-phe_5_signal51.511574
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1110.570923
RawQ2.347400
Spike_AFFX-r2-Bs-lys_5_signal28.797482
Signal(A)5.175076
%A38.364754
Signal(All)148.484528
Corner+Avg:78,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal257.390289
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal53.086590
Spike_AFFX-r2-Ec-bioD_avg-signal886.331970
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.868477
Spike_AFFX-r2-Bs-lys_avg-signal27.666763
Spike_AFFX-r2-P1-cre_avg-signal3640.451416
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.766769
Spike_AFFX-r2-Bs-thr_3_signal109.405136
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-signal51.124908
Spike_AFFX-r2-Bs-dap_3_signal246.676651
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.677364
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal266.225800
#M403
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.080341
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.966812
Spike_AFFX-r2-Bs-thr_M_signal110.923279
Signal(P)244.090836
Spike_AFFX-r2-Bs-phe_3-5-ratio1.030576
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5378,Count:9
Spike_AFFX-r2-P1-cre_5_signal3307.697754
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8751
Signal(M)20.695608
BackgroundAvg:81.39,Std:0.42,Min:79.4,Max:82.3
Spike_AFFX-r2-Ec-bioC_avg-signal261.808044
Spike_AFFX-r2-Bs-dap_avg-signal169.862289
Spike_AFFX-r2-Bs-dap_3-5-ratio2.981645
Spike_AFFX-r2-Ec-bioB_5_signal58.175640
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.818276
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-16_x_18_6-wks_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 ("Diaz_542-16_x_18_6-wks_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: Diaz_542-16_x_18_6-wks_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 6 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:1.151437
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-ratio1.202767
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.778069
Spike_AFFX-r2-Bs-dap_5_signal127.170799
NoiseAvg:2.07,Std:0.05,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal82.323631
#P13246
Spike_AFFX-r2-Bs-phe_M_signal57.133980
Corner-Avg:5628,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal129.259872
Spike_AFFX-r2-Ec-bioB_3_signal84.036018
Spike_AFFX-r2-Bs-lys_M_signal25.899555
Spike_AFFX-r2-P1-cre_3_signal6863.999023
Spike_AFFX-r2-Bs-lys_3-5-ratio1.638324
Spike_AFFX-r2-Bs-dap_M_signal240.669144
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.785653
Spike_AFFX-r2-Ec-bioB_avg-signal107.100586
Spike_AFFX-r2-Bs-thr_avg-signal156.307510
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1274.291626
Spike_AFFX-r2-Bs-phe_5_signal78.612335
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1933.969604
RawQ2.037725
Spike_AFFX-r2-Bs-lys_5_signal33.522064
Signal(A)6.014147
%A40.276196
Signal(All)156.334671
Corner+Avg:67,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal487.133270
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal77.836143
Spike_AFFX-r2-Ec-bioD_avg-signal1604.130615
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.071022
Spike_AFFX-r2-Bs-lys_avg-signal38.113873
Spike_AFFX-r2-P1-cre_avg-signal6285.418945
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.652784
Spike_AFFX-r2-Bs-thr_3_signal229.325104
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal71.194153
Spike_AFFX-r2-Bs-dap_3_signal359.965332
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.517682
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal424.177368
#M377
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal54.920002
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.148419
Spike_AFFX-r2-Bs-thr_M_signal157.273804
Signal(P)264.406647
Spike_AFFX-r2-Bs-phe_3-5-ratio0.990126
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3615,Count:9
Spike_AFFX-r2-P1-cre_5_signal5706.838867
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9187
Signal(M)22.312428
BackgroundAvg:75.25,Std:0.75,Min:73.3,Max:76.8
Spike_AFFX-r2-Ec-bioC_avg-signal455.655334
Spike_AFFX-r2-Bs-dap_avg-signal242.601746
Spike_AFFX-r2-Bs-dap_3-5-ratio2.830566
Spike_AFFX-r2-Ec-bioB_5_signal108.005867
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.151437
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-17_x_13_18_6-wks_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 ("Diaz_542-17_x_13_18_6-wks_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: Diaz_542-17_x_13_18_6-wks_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: vtc2xabi4
Stock Code:
Growth Conditions:
ProtocolPlants were grown for 6 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Genetic Variation: induced mutation mutation in
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.626547
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-ratio1.382051
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.014383
Spike_AFFX-r2-Bs-dap_5_signal85.894814
NoiseAvg:2.26,Std:0.06,Min:2.1,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal45.421982
#P14281
Spike_AFFX-r2-Bs-phe_M_signal46.807976
Corner-Avg:6649,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.778198
Spike_AFFX-r2-Ec-bioB_3_signal64.116203
Spike_AFFX-r2-Bs-lys_M_signal12.180201
Spike_AFFX-r2-P1-cre_3_signal5452.724121
Spike_AFFX-r2-Bs-lys_3-5-ratio1.616358
Spike_AFFX-r2-Bs-dap_M_signal215.956284
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.277621
Spike_AFFX-r2-Ec-bioB_avg-signal72.700508
Spike_AFFX-r2-Bs-thr_avg-signal94.064857
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal883.087097
Spike_AFFX-r2-Bs-phe_5_signal52.361366
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1267.699707
RawQ2.116575
Spike_AFFX-r2-Bs-lys_5_signal26.518475
Signal(A)3.652628
%A35.826393
Signal(All)150.431534
Corner+Avg:83,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal301.003906
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal47.279018
Spike_AFFX-r2-Ec-bioD_avg-signal1075.393433
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.608505
Spike_AFFX-r2-Bs-lys_avg-signal27.187342
Spike_AFFX-r2-P1-cre_avg-signal4699.054199
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.565103
Spike_AFFX-r2-Bs-thr_3_signal148.876022
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.816120
Spike_AFFX-r2-Bs-dap_3_signal255.317017
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.435532
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal254.931992
#M357
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.863358
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.180722
Spike_AFFX-r2-Bs-thr_M_signal87.896561
Signal(P)237.796829
Spike_AFFX-r2-Bs-phe_3-5-ratio0.902937
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4398,Count:9
Spike_AFFX-r2-P1-cre_5_signal3945.384521
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8172
Signal(M)15.454886
BackgroundAvg:77.70,Std:0.72,Min:75.6,Max:79.2
Spike_AFFX-r2-Ec-bioC_avg-signal277.967957
Spike_AFFX-r2-Bs-dap_avg-signal185.722717
Spike_AFFX-r2-Bs-dap_3-5-ratio2.972438
Spike_AFFX-r2-Ec-bioB_5_signal63.207123
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.626547
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-18_Col-0_12-wks_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Diaz_542-18_Col-0_12-wks_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: Diaz_542-18_Col-0_12-wks_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.957568
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-ratio0.960304
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.088942
Spike_AFFX-r2-Bs-dap_5_signal145.399826
NoiseAvg:2.14,Std:0.17,Min:1.9,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal66.726517
#P13760
Spike_AFFX-r2-Bs-phe_M_signal75.926971
Corner-Avg:7065,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal117.669083
Spike_AFFX-r2-Ec-bioB_3_signal107.817039
Spike_AFFX-r2-Bs-lys_M_signal28.811897
Spike_AFFX-r2-P1-cre_3_signal5449.898438
Spike_AFFX-r2-Bs-lys_3-5-ratio1.442808
Spike_AFFX-r2-Bs-dap_M_signal333.137512
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.709511
Spike_AFFX-r2-Ec-bioB_avg-signal108.165627
Spike_AFFX-r2-Bs-thr_avg-signal136.731979
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1138.219116
Spike_AFFX-r2-Bs-phe_5_signal102.007072
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1991.537231
RawQ2.067483
Spike_AFFX-r2-Bs-lys_5_signal35.314438
Signal(A)4.918828
%A37.878124
Signal(All)154.686447
Corner+Avg:78,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal387.571747
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal69.404587
Spike_AFFX-r2-Ec-bioD_avg-signal1564.878174
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.324421
Spike_AFFX-r2-Bs-lys_avg-signal38.359432
Spike_AFFX-r2-P1-cre_avg-signal5562.538086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.797457
Spike_AFFX-r2-Bs-thr_3_signal180.796249
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal82.446205
Spike_AFFX-r2-Bs-dap_3_signal379.864532
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.749696
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal336.526764
#M410
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.951962
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.151682
Spike_AFFX-r2-Bs-thr_M_signal162.673157
Signal(P)252.790848
Spike_AFFX-r2-Bs-phe_3-5-ratio0.680390
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5835,Count:9
Spike_AFFX-r2-P1-cre_5_signal5675.178223
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8640
Signal(M)18.285610
BackgroundAvg:49.08,Std:0.42,Min:48.3,Max:50.4
Spike_AFFX-r2-Ec-bioC_avg-signal362.049255
Spike_AFFX-r2-Bs-dap_avg-signal286.133972
Spike_AFFX-r2-Bs-dap_3-5-ratio2.612551
Spike_AFFX-r2-Ec-bioB_5_signal99.010780
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.957568
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-19_Col-0_12-wks_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 ("Diaz_542-19_Col-0_12-wks_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: Diaz_542-19_Col-0_12-wks_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Tissue: whole plant
Additional Organism Information:
Sample Description
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:1.0333
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-ratio1.356481
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.019620
Spike_AFFX-r2-Bs-dap_5_signal109.442528
NoiseAvg:1.98,Std:0.05,Min:1.9,Max:2.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal68.834007
#P13397
Spike_AFFX-r2-Bs-phe_M_signal60.290264
Corner-Avg:5558,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal106.186028
Spike_AFFX-r2-Ec-bioB_3_signal79.055412
Spike_AFFX-r2-Bs-lys_M_signal22.783998
Spike_AFFX-r2-P1-cre_3_signal6387.435547
Spike_AFFX-r2-Bs-lys_3-5-ratio1.306802
Spike_AFFX-r2-Bs-dap_M_signal231.183670
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.872328
Spike_AFFX-r2-Ec-bioB_avg-signal87.591881
Spike_AFFX-r2-Bs-thr_avg-signal131.239471
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1123.060669
Spike_AFFX-r2-Bs-phe_5_signal66.797432
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1754.828491
RawQ1.964821
Spike_AFFX-r2-Bs-lys_5_signal25.439924
Signal(A)5.753846
%A39.311707
Signal(All)158.065811
Corner+Avg:65,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal345.728333
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal76.115768
Spike_AFFX-r2-Ec-bioD_avg-signal1438.944580
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.733013
Spike_AFFX-r2-Bs-lys_avg-signal27.156290
Spike_AFFX-r2-P1-cre_avg-signal5548.131836
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.955283
Spike_AFFX-r2-Bs-thr_3_signal197.713852
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal67.734489
Spike_AFFX-r2-Bs-dap_3_signal294.088013
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.562541
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal344.712799
#M446
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.244946
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.002946
Spike_AFFX-r2-Bs-thr_M_signal127.170563
Signal(P)264.580872
Spike_AFFX-r2-Bs-phe_3-5-ratio1.139501
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3877,Count:9
Spike_AFFX-r2-P1-cre_5_signal4708.827637
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8967
Signal(M)20.843847
BackgroundAvg:48.06,Std:0.20,Min:47.6,Max:48.7
Spike_AFFX-r2-Ec-bioC_avg-signal345.220581
Spike_AFFX-r2-Bs-dap_avg-signal211.571396
Spike_AFFX-r2-Bs-dap_3-5-ratio2.687146
Spike_AFFX-r2-Ec-bioB_5_signal77.534203
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.033300
NF1.000000
HZ4
Tau0.015000

Slide: Diaz_542-20_Col-0_12-wks_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 ("Diaz_542-20_Col-0_12-wks_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: Diaz_542-20_Col-0_12-wks_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolPlants were grown for 12 weeks at 22oC under low (250 µmol m-2 s-1) light with a 10-h photoperiod.
Soil ConstituentsSinclair SHL Multi Purpose Peat Based Compost.
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
Lighting10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)5.10
Tissue: whole plant
Additional Organism Information:
Sample Description
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:0.893647
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-ratio1.312575
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.158844
Spike_AFFX-r2-Bs-dap_5_signal117.047539
NoiseAvg:2.01,Std:0.05,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal74.686890
#P13782
Spike_AFFX-r2-Bs-phe_M_signal66.475227
Corner-Avg:6600,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.562286
Spike_AFFX-r2-Ec-bioB_3_signal85.910858
Spike_AFFX-r2-Bs-lys_M_signal22.446329
Spike_AFFX-r2-P1-cre_3_signal6582.888184
Spike_AFFX-r2-Bs-lys_3-5-ratio1.683257
Spike_AFFX-r2-Bs-dap_M_signal290.388885
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.929245
Spike_AFFX-r2-Ec-bioB_avg-signal87.536049
Spike_AFFX-r2-Bs-thr_avg-signal150.198807
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1162.907715
Spike_AFFX-r2-Bs-phe_5_signal73.861023
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1812.302368
RawQ2.079851
Spike_AFFX-r2-Bs-lys_5_signal32.652237
Signal(A)4.289979
%A37.882507
Signal(All)159.759109
Corner+Avg:71,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal352.731750
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal83.404587
Spike_AFFX-r2-Ec-bioD_avg-signal1487.604980
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.420868
Spike_AFFX-r2-Bs-lys_avg-signal36.686893
Spike_AFFX-r2-P1-cre_avg-signal5799.067871
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.696624
Spike_AFFX-r2-Bs-thr_3_signal218.776215
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal74.580284
Spike_AFFX-r2-Bs-dap_3_signal421.285980
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.558423
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal339.765900
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal54.962109
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.038161
Spike_AFFX-r2-Bs-thr_M_signal157.133347
Signal(P)261.216583
Spike_AFFX-r2-Bs-phe_3-5-ratio1.129210
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4326,Count:9
Spike_AFFX-r2-P1-cre_5_signal5015.247559
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8641
Signal(M)17.956068
BackgroundAvg:51.17,Std:0.33,Min:50.2,Max:52.1
Spike_AFFX-r2-Ec-bioC_avg-signal346.248840
Spike_AFFX-r2-Bs-dap_avg-signal276.240814
Spike_AFFX-r2-Bs-dap_3-5-ratio3.599272
Spike_AFFX-r2-Ec-bioB_5_signal74.134995
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.893647
NF1.000000
HZ4
Tau0.015000


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