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Experiment: L.C EXP1/K.L EXP2

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-571

Experiment 1Investigator: L. CivaleThe aim is to characterise and compare the gene expression profiles of Arabidopsis roots of mature plants treated to hypoxic stress (Sparged with 3% O2 Gas) grown in hydroponic culture, in wild-type (Col-0) and nia1 T-DNA insertion mutant line plants(SALK_148487C). NIA1 is the minor isoform of nitrate reductase in Arabidopsis.Experiment 2Investigator: K. LewandowskiThe aim is to characterise and compare the gene expression profiles of leaf and meristem tissue taken from wild-type (Col-0) Arabidopsis plants and a transgenic line overexpressing a potential novel miRNA, just before the transition to reproductive growth.

About the Experimenter

Name:Mr Leon Civale
Head of Lab Name:Prof Steven Neill
Lab:
Address:Centre for Research in Plant Science (CRIPS), Faculty of Applied Sciences, University of the West of England
Frenchay Campus, Coldharbour Lane, Bristol, , BS16 1QY, UNITED KINGDOM
Postcode:
Country:
 

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

About this Experiment

Experiment Type: genetic_modification
Number of Slides:24
 
Experimental Parameters:
parametergenetic_modification
parameterdevelopmental_stage
parameterorganism_part
parameterstrain_or_line
parametergene_knock_out
otherfactorHypoxia
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Civale: L.C EXP1/K.L EXP2

Slide: Civale_571-1_Normoxia-24hrs-Col-0_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Civale_571-1_Normoxia-24hrs-Col-0_Rep1_ATH1") was made from "" 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: Civale_571-1_Normoxia-24hrs-Col-0_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.546502
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-ratio1.260844
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.136172
Spike_AFFX-r2-Bs-dap_5_signal42.041901
NoiseAvg:2.61,Std:0.07,Min:2.5,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_signal15.107470
#P15260
Spike_AFFX-r2-Bs-phe_M_signal15.945160
Corner-Avg:10287,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal113.717545
Spike_AFFX-r2-Ec-bioB_3_signal63.033607
Spike_AFFX-r2-Bs-lys_M_signal19.163292
Spike_AFFX-r2-P1-cre_3_signal4035.636719
Spike_AFFX-r2-Bs-lys_3-5-ratio2.480438
Spike_AFFX-r2-Bs-dap_M_signal122.476646
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.849797
Spike_AFFX-r2-Ec-bioB_avg-signal77.410027
Spike_AFFX-r2-Bs-thr_avg-signal47.413544
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal716.750305
Spike_AFFX-r2-Bs-phe_5_signal21.287991
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1161.281006
RawQ2.340294
Spike_AFFX-r2-Bs-lys_5_signal14.574930
Signal(A)3.391293
%A31.613327
Signal(All)137.953369
Corner+Avg:159,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal229.054077
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.355703
Spike_AFFX-r2-Ec-bioD_avg-signal939.015625
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.900482
Spike_AFFX-r2-Bs-lys_avg-signal23.296808
Spike_AFFX-r2-P1-cre_avg-signal3618.189453
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.486190
Spike_AFFX-r2-Bs-thr_3_signal88.375633
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-signal22.196283
Spike_AFFX-r2-Bs-dap_3_signal193.206512
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.620203
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal243.756119
#M339
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.152203
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.939685
Spike_AFFX-r2-Bs-thr_M_signal38.757523
Signal(P)204.314667
Spike_AFFX-r2-Bs-phe_3-5-ratio1.378980
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8069,Count:9
Spike_AFFX-r2-P1-cre_5_signal3200.742432
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7211
Signal(M)13.037821
BackgroundAvg:56.87,Std:0.73,Min:55.2,Max:59.2
Spike_AFFX-r2-Ec-bioC_avg-signal236.405090
Spike_AFFX-r2-Bs-dap_avg-signal119.241692
Spike_AFFX-r2-Bs-dap_3-5-ratio4.595571
Spike_AFFX-r2-Ec-bioB_5_signal55.478916
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.546502
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-2_Normoxia-24hrs-Col-0_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-2_Normoxia-24hrs-Col-0_Rep2_ATH1") was made from "" 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: Civale_571-2_Normoxia-24hrs-Col-0_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.323149
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-ratio1.082880
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.825301
Spike_AFFX-r2-Bs-dap_5_signal46.957024
NoiseAvg:3.06,Std:0.10,Min:2.8,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.971149
#P15815
Spike_AFFX-r2-Bs-phe_M_signal17.448450
Corner-Avg:10497,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.085983
Spike_AFFX-r2-Ec-bioB_3_signal42.477974
Spike_AFFX-r2-Bs-lys_M_signal10.611101
Spike_AFFX-r2-P1-cre_3_signal2702.140381
Spike_AFFX-r2-Bs-lys_3-5-ratio1.786645
Spike_AFFX-r2-Bs-dap_M_signal126.164650
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.549683
Spike_AFFX-r2-Ec-bioB_avg-signal57.011211
Spike_AFFX-r2-Bs-thr_avg-signal47.844204
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal424.513458
Spike_AFFX-r2-Bs-phe_5_signal16.073494
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal687.346680
RawQ2.713202
Spike_AFFX-r2-Bs-lys_5_signal16.294127
Signal(A)2.244883
%A29.386234
Signal(All)133.979446
Corner+Avg:172,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.950943
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.670198
Spike_AFFX-r2-Ec-bioD_avg-signal555.930054
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.333626
Spike_AFFX-r2-Bs-lys_avg-signal18.672348
Spike_AFFX-r2-P1-cre_avg-signal2598.733398
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.280140
Spike_AFFX-r2-Bs-thr_3_signal88.634819
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-signal18.064047
Spike_AFFX-r2-Bs-dap_3_signal188.292801
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.619140
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal147.132904
#M292
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.111813
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.080322
Spike_AFFX-r2-Bs-thr_M_signal38.926643
Signal(P)192.110046
Spike_AFFX-r2-Bs-phe_3-5-ratio1.285980
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8133,Count:9
Spike_AFFX-r2-P1-cre_5_signal2495.326660
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6703
Signal(M)9.600385
BackgroundAvg:64.79,Std:0.74,Min:62.5,Max:66.8
Spike_AFFX-r2-Ec-bioC_avg-signal153.041931
Spike_AFFX-r2-Bs-dap_avg-signal120.471497
Spike_AFFX-r2-Bs-dap_3-5-ratio4.009896
Spike_AFFX-r2-Ec-bioB_5_signal51.469669
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.323149
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-3_Normoxia-24hrs-Col-0_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-3_Normoxia-24hrs-Col-0_Rep3_ATH1") was made from "" 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: Civale_571-3_Normoxia-24hrs-Col-0_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.323829
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-ratio1.138797
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.007884
Spike_AFFX-r2-Bs-dap_5_signal33.302818
NoiseAvg:2.87,Std:0.11,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.842322
#P16089
Spike_AFFX-r2-Bs-phe_M_signal14.639600
Corner-Avg:9785,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal72.778580
Spike_AFFX-r2-Ec-bioB_3_signal47.754547
Spike_AFFX-r2-Bs-lys_M_signal11.500794
Spike_AFFX-r2-P1-cre_3_signal2984.534424
Spike_AFFX-r2-Bs-lys_3-5-ratio1.411256
Spike_AFFX-r2-Bs-dap_M_signal97.467010
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.639677
Spike_AFFX-r2-Ec-bioB_avg-signal55.971378
Spike_AFFX-r2-Bs-thr_avg-signal40.785748
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal491.218750
Spike_AFFX-r2-Bs-phe_5_signal22.352978
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal724.488159
RawQ2.554211
Spike_AFFX-r2-Bs-lys_5_signal12.740778
Signal(A)2.001387
%A28.220079
Signal(All)132.623047
Corner+Avg:160,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal178.653687
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.158598
Spike_AFFX-r2-Ec-bioD_avg-signal607.853455
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.534851
Spike_AFFX-r2-Bs-lys_avg-signal14.074023
Spike_AFFX-r2-P1-cre_avg-signal2802.656250
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.245068
Spike_AFFX-r2-Bs-thr_3_signal72.426552
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-signal20.383726
Spike_AFFX-r2-Bs-dap_3_signal178.062424
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.474879
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal159.958847
#M284
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.980494
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.116873
Spike_AFFX-r2-Bs-thr_M_signal37.088367
Signal(P)187.076706
Spike_AFFX-r2-Bs-phe_3-5-ratio1.080778
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7479,Count:9
Spike_AFFX-r2-P1-cre_5_signal2620.778320
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6437
Signal(M)8.351445
BackgroundAvg:61.47,Std:0.55,Min:60.0,Max:63.0
Spike_AFFX-r2-Ec-bioC_avg-signal169.306274
Spike_AFFX-r2-Bs-dap_avg-signal102.944084
Spike_AFFX-r2-Bs-dap_3-5-ratio5.346767
Spike_AFFX-r2-Ec-bioB_5_signal47.381008
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.323829
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-4_Hypoxia-24hrs-Col-0_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Civale_571-4_Hypoxia-24hrs-Col-0_Rep1_ATH1") was made from "" 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: Civale_571-4_Hypoxia-24hrs-Col-0_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.326447
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-ratio1.092815
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.010827
Spike_AFFX-r2-Bs-dap_5_signal40.246456
NoiseAvg:2.65,Std:0.09,Min:2.4,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_signal15.361476
#P16036
Spike_AFFX-r2-Bs-phe_M_signal15.433130
Corner-Avg:9766,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal69.201958
Spike_AFFX-r2-Ec-bioB_3_signal46.730083
Spike_AFFX-r2-Bs-lys_M_signal8.322165
Spike_AFFX-r2-P1-cre_3_signal2839.008057
Spike_AFFX-r2-Bs-lys_3-5-ratio1.824747
Spike_AFFX-r2-Bs-dap_M_signal131.147583
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.888614
Spike_AFFX-r2-Ec-bioB_avg-signal54.053860
Spike_AFFX-r2-Bs-thr_avg-signal50.671829
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal467.735992
Spike_AFFX-r2-Bs-phe_5_signal17.577135
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal735.310608
RawQ2.423347
Spike_AFFX-r2-Bs-lys_5_signal13.253495
Signal(A)1.878950
%A28.509426
Signal(All)134.172714
Corner+Avg:152,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal191.812668
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.674534
Spike_AFFX-r2-Ec-bioD_avg-signal601.523315
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.302498
Spike_AFFX-r2-Bs-lys_avg-signal15.253314
Spike_AFFX-r2-P1-cre_avg-signal2718.447021
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.188075
Spike_AFFX-r2-Bs-thr_3_signal90.457802
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-signal18.228266
Spike_AFFX-r2-Bs-dap_3_signal186.202728
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.572063
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal167.189301
#M271
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.184280
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.147278
Spike_AFFX-r2-Bs-thr_M_signal46.196209
Signal(P)189.939697
Spike_AFFX-r2-Bs-phe_3-5-ratio1.233110
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7293,Count:9
Spike_AFFX-r2-P1-cre_5_signal2597.885986
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6503
Signal(M)8.810763
BackgroundAvg:56.04,Std:0.65,Min:54.4,Max:57.6
Spike_AFFX-r2-Ec-bioC_avg-signal179.500977
Spike_AFFX-r2-Bs-dap_avg-signal119.198921
Spike_AFFX-r2-Bs-dap_3-5-ratio4.626562
Spike_AFFX-r2-Ec-bioB_5_signal46.229538
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.326447
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-5_Hypoxia-24hrs-Col-0_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-5_Hypoxia-24hrs-Col-0_Rep2_ATH1") was made from "" 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: Civale_571-5_Hypoxia-24hrs-Col-0_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.430082
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-ratio0.914490
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.062665
Spike_AFFX-r2-Bs-dap_5_signal50.789928
NoiseAvg:2.61,Std:0.07,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_signal17.945654
#P15519
Spike_AFFX-r2-Bs-phe_M_signal19.908497
Corner-Avg:11700,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.355354
Spike_AFFX-r2-Ec-bioB_3_signal70.869911
Spike_AFFX-r2-Bs-lys_M_signal21.093868
Spike_AFFX-r2-P1-cre_3_signal2823.630127
Spike_AFFX-r2-Bs-lys_3-5-ratio1.334975
Spike_AFFX-r2-Bs-dap_M_signal125.114845
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.487838
Spike_AFFX-r2-Ec-bioB_avg-signal76.638657
Spike_AFFX-r2-Bs-thr_avg-signal39.458347
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal591.073547
Spike_AFFX-r2-Bs-phe_5_signal31.453251
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal945.625183
RawQ2.397059
Spike_AFFX-r2-Bs-lys_5_signal17.886467
Signal(A)2.459333
%A30.609383
Signal(All)135.190582
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal230.699036
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.623419
Spike_AFFX-r2-Ec-bioD_avg-signal768.349365
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.035950
Spike_AFFX-r2-Bs-lys_avg-signal20.952772
Spike_AFFX-r2-P1-cre_avg-signal2955.643066
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.354669
Spike_AFFX-r2-Bs-thr_3_signal62.591526
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.328390
Spike_AFFX-r2-Bs-dap_3_signal209.383545
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.599844
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal187.569000
#M309
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.877981
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.229942
Spike_AFFX-r2-Bs-thr_M_signal37.837852
Signal(P)197.404053
Spike_AFFX-r2-Bs-phe_3-5-ratio0.973617
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10258,Count:9
Spike_AFFX-r2-P1-cre_5_signal3087.655762
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6982
Signal(M)9.749634
BackgroundAvg:57.46,Std:1.00,Min:55.0,Max:60.7
Spike_AFFX-r2-Ec-bioC_avg-signal209.134018
Spike_AFFX-r2-Bs-dap_avg-signal128.429428
Spike_AFFX-r2-Bs-dap_3-5-ratio4.122540
Spike_AFFX-r2-Ec-bioB_5_signal66.690704
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.430082
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-6_Hypoxia-24hrs-Col-0_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-6_Hypoxia-24hrs-Col-0_Rep3_ATH1") was made from "" 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: Civale_571-6_Hypoxia-24hrs-Col-0_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.555955
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-ratio0.785260
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.968007
Spike_AFFX-r2-Bs-dap_5_signal42.490219
NoiseAvg:2.47,Std:0.12,Min:2.1,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.390097
#P14991
Spike_AFFX-r2-Bs-phe_M_signal17.855892
Corner-Avg:9468,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal109.101143
Spike_AFFX-r2-Ec-bioB_3_signal62.957348
Spike_AFFX-r2-Bs-lys_M_signal13.004873
Spike_AFFX-r2-P1-cre_3_signal3019.831543
Spike_AFFX-r2-Bs-lys_3-5-ratio1.786330
Spike_AFFX-r2-Bs-dap_M_signal101.507278
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.725657
Spike_AFFX-r2-Ec-bioB_avg-signal79.032204
Spike_AFFX-r2-Bs-thr_avg-signal49.610428
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal591.353638
Spike_AFFX-r2-Bs-phe_5_signal22.571228
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1015.504578
RawQ2.453882
Spike_AFFX-r2-Bs-lys_5_signal15.816099
Signal(A)3.255095
%A32.722488
Signal(All)140.761002
Corner+Avg:148,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal260.750763
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.211147
Spike_AFFX-r2-Ec-bioD_avg-signal803.429077
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.721176
Spike_AFFX-r2-Bs-lys_avg-signal19.024584
Spike_AFFX-r2-P1-cre_avg-signal3432.738770
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.556335
Spike_AFFX-r2-Bs-thr_3_signal72.240845
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-signal21.879423
Spike_AFFX-r2-Bs-dap_3_signal202.792374
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.717254
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal221.410980
#M355
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.252777
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.177678
Spike_AFFX-r2-Bs-thr_M_signal57.200340
Signal(P)212.263626
Spike_AFFX-r2-Bs-phe_3-5-ratio1.116959
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7887,Count:9
Spike_AFFX-r2-P1-cre_5_signal3845.645752
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7464
Signal(M)12.445807
BackgroundAvg:54.34,Std:0.70,Min:51.7,Max:55.8
Spike_AFFX-r2-Ec-bioC_avg-signal241.080872
Spike_AFFX-r2-Bs-dap_avg-signal115.596619
Spike_AFFX-r2-Bs-dap_3-5-ratio4.772684
Spike_AFFX-r2-Ec-bioB_5_signal65.038116
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.555955
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-7_Normoxia-24hrs-nia1_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Civale_571-7_Normoxia-24hrs-nia1_Rep1_ATH1") was made from "" 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: Civale_571-7_Normoxia-24hrs-nia1_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.328864
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-ratio1.021822
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.779549
Spike_AFFX-r2-Bs-dap_5_signal35.198357
NoiseAvg:2.84,Std:0.13,Min:2.5,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.431628
#P15753
Spike_AFFX-r2-Bs-phe_M_signal18.011599
Corner-Avg:10133,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal64.356163
Spike_AFFX-r2-Ec-bioB_3_signal39.292030
Spike_AFFX-r2-Bs-lys_M_signal12.606544
Spike_AFFX-r2-P1-cre_3_signal2553.631104
Spike_AFFX-r2-Bs-lys_3-5-ratio2.060189
Spike_AFFX-r2-Bs-dap_M_signal98.166359
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.311803
Spike_AFFX-r2-Ec-bioB_avg-signal51.350574
Spike_AFFX-r2-Bs-thr_avg-signal44.033478
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal439.750763
Spike_AFFX-r2-Bs-phe_5_signal14.180392
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal655.091858
RawQ2.379707
Spike_AFFX-r2-Bs-lys_5_signal12.947536
Signal(A)2.690194
%A29.482683
Signal(All)135.674133
Corner+Avg:171,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal192.480743
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.125097
Spike_AFFX-r2-Ec-bioD_avg-signal547.421326
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.061813
Spike_AFFX-r2-Bs-lys_avg-signal17.409487
Spike_AFFX-r2-P1-cre_avg-signal2526.363281
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.455502
Spike_AFFX-r2-Bs-thr_3_signal86.705635
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-signal18.772364
Spike_AFFX-r2-Bs-dap_3_signal203.542526
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.489689
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal150.531815
#M332
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.674376
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.278672
Spike_AFFX-r2-Bs-thr_M_signal34.963169
Signal(P)195.076736
Spike_AFFX-r2-Bs-phe_3-5-ratio1.701300
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7358,Count:9
Spike_AFFX-r2-P1-cre_5_signal2499.095459
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6725
Signal(M)10.818574
BackgroundAvg:55.82,Std:0.50,Min:54.9,Max:57.2
Spike_AFFX-r2-Ec-bioC_avg-signal171.506287
Spike_AFFX-r2-Bs-dap_avg-signal112.302422
Spike_AFFX-r2-Bs-dap_3-5-ratio5.782728
Spike_AFFX-r2-Ec-bioB_5_signal50.403538
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.328864
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-8_Normoxia-24hrs-nia1_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 ("Civale_571-8_Normoxia-24hrs-nia1_Rep2_ATH1") was made from "" 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: Civale_571-8_Normoxia-24hrs-nia1_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.521078
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-ratio0.966997
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.943294
Spike_AFFX-r2-Bs-dap_5_signal26.286278
NoiseAvg:2.59,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_signal12.773561
#P15233
Spike_AFFX-r2-Bs-phe_M_signal14.913822
Corner-Avg:7568,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal70.773659
Spike_AFFX-r2-Ec-bioB_3_signal35.888035
Spike_AFFX-r2-Bs-lys_M_signal7.543859
Spike_AFFX-r2-P1-cre_3_signal2465.893555
Spike_AFFX-r2-Bs-lys_3-5-ratio1.663367
Spike_AFFX-r2-Bs-dap_M_signal89.799141
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.876852
Spike_AFFX-r2-Ec-bioB_avg-signal48.235706
Spike_AFFX-r2-Bs-thr_avg-signal30.789194
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal422.807159
Spike_AFFX-r2-Bs-phe_5_signal13.308701
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal677.294678
RawQ2.416708
Spike_AFFX-r2-Bs-lys_5_signal6.522669
Signal(A)3.234346
%A31.591408
Signal(All)137.474121
Corner+Avg:121,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal161.617554
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.188787
Spike_AFFX-r2-Ec-bioD_avg-signal550.050903
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.782112
Spike_AFFX-r2-Bs-lys_avg-signal8.305372
Spike_AFFX-r2-P1-cre_avg-signal2507.973633
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal49.521198
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-signal15.137103
Spike_AFFX-r2-Bs-dap_3_signal147.124649
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.601900
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal169.026077
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal10.849589
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.956169
Spike_AFFX-r2-Bs-thr_M_signal30.072824
Signal(P)204.027451
Spike_AFFX-r2-Bs-phe_3-5-ratio1.291545
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5459,Count:9
Spike_AFFX-r2-P1-cre_5_signal2550.053467
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7206
Signal(M)12.204368
BackgroundAvg:56.62,Std:0.47,Min:55.7,Max:58.0
Spike_AFFX-r2-Ec-bioC_avg-signal165.321808
Spike_AFFX-r2-Bs-dap_avg-signal87.736694
Spike_AFFX-r2-Bs-dap_3-5-ratio5.597013
Spike_AFFX-r2-Ec-bioB_5_signal38.045422
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.521078
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-9_Normoxia-24hrs-nia1_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 ("Civale_571-9_Normoxia-24hrs-nia1_Rep3_ATH1") was made from "" 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: Civale_571-9_Normoxia-24hrs-nia1_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.496006
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-ratio0.896525
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.759223
Spike_AFFX-r2-Bs-dap_5_signal30.608173
NoiseAvg:2.51,Std:0.06,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_signal18.334911
#P15447
Spike_AFFX-r2-Bs-phe_M_signal13.468105
Corner-Avg:8988,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.819023
Spike_AFFX-r2-Ec-bioB_3_signal38.973911
Spike_AFFX-r2-Bs-lys_M_signal9.597190
Spike_AFFX-r2-P1-cre_3_signal2606.806641
Spike_AFFX-r2-Bs-lys_3-5-ratio1.747195
Spike_AFFX-r2-Bs-dap_M_signal83.752434
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.331907
Spike_AFFX-r2-Ec-bioB_avg-signal58.708958
Spike_AFFX-r2-Bs-thr_avg-signal31.471029
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal540.274048
Spike_AFFX-r2-Bs-phe_5_signal16.110836
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal777.905151
RawQ2.379507
Spike_AFFX-r2-Bs-lys_5_signal9.787316
Signal(A)2.906052
%A30.942570
Signal(All)135.654419
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal179.728470
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.576532
Spike_AFFX-r2-Ec-bioD_avg-signal659.089600
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.720299
Spike_AFFX-r2-Bs-lys_avg-signal12.161618
Spike_AFFX-r2-P1-cre_avg-signal2757.242676
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.337133
Spike_AFFX-r2-Bs-thr_3_signal42.755299
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-signal17.385159
Spike_AFFX-r2-Bs-dap_3_signal126.855278
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.439834
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.551437
#M305
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.100351
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.029659
Spike_AFFX-r2-Bs-thr_M_signal33.322872
Signal(P)198.771240
Spike_AFFX-r2-Bs-phe_3-5-ratio1.401326
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6417,Count:9
Spike_AFFX-r2-P1-cre_5_signal2907.678711
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7058
Signal(M)10.974468
BackgroundAvg:56.12,Std:0.42,Min:55.1,Max:57.5
Spike_AFFX-r2-Ec-bioC_avg-signal177.139954
Spike_AFFX-r2-Bs-dap_avg-signal80.405296
Spike_AFFX-r2-Bs-dap_3-5-ratio4.144490
Spike_AFFX-r2-Ec-bioB_5_signal51.333939
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.496006
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-10_Hypoxia-24hrs-nia1_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Civale_571-10_Hypoxia-24hrs-nia1_Rep1_ATH1") was made from "" 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: Civale_571-10_Hypoxia-24hrs-nia1_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.723459
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-ratio1.150506
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.202006
Spike_AFFX-r2-Bs-dap_5_signal46.102562
NoiseAvg:2.37,Std:0.07,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_signal26.209097
#P14941
Spike_AFFX-r2-Bs-phe_M_signal13.079477
Corner-Avg:7404,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.638382
Spike_AFFX-r2-Ec-bioB_3_signal67.859283
Spike_AFFX-r2-Bs-lys_M_signal11.331797
Spike_AFFX-r2-P1-cre_3_signal3399.081055
Spike_AFFX-r2-Bs-lys_3-5-ratio1.711492
Spike_AFFX-r2-Bs-dap_M_signal102.654701
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.788038
Spike_AFFX-r2-Ec-bioB_avg-signal67.317558
Spike_AFFX-r2-Bs-thr_avg-signal57.853729
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal528.918030
Spike_AFFX-r2-Bs-phe_5_signal19.530046
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal806.457275
RawQ2.238899
Spike_AFFX-r2-Bs-lys_5_signal13.885719
Signal(A)4.343099
%A32.753178
Signal(All)137.458679
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal242.456299
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.295847
Spike_AFFX-r2-Ec-bioD_avg-signal667.687622
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.501976
Spike_AFFX-r2-Bs-lys_avg-signal16.327604
Spike_AFFX-r2-P1-cre_avg-signal3176.751953
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.744849
Spike_AFFX-r2-Bs-thr_3_signal99.281044
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.301790
Spike_AFFX-r2-Bs-dap_3_signal147.792236
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.524730
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal229.503235
#M398
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.765293
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.056440
Spike_AFFX-r2-Bs-thr_M_signal48.071049
Signal(P)207.264679
Spike_AFFX-r2-Bs-phe_3-5-ratio1.295227
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6894,Count:9
Spike_AFFX-r2-P1-cre_5_signal2954.422607
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7471
Signal(M)15.687773
BackgroundAvg:52.46,Std:0.50,Min:51.4,Max:54.0
Spike_AFFX-r2-Ec-bioC_avg-signal235.979767
Spike_AFFX-r2-Bs-dap_avg-signal98.849831
Spike_AFFX-r2-Bs-dap_3-5-ratio3.205727
Spike_AFFX-r2-Ec-bioB_5_signal56.455017
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.723459
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-11_Hypoxia-24hrs-nia1_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 ("Civale_571-11_Hypoxia-24hrs-nia1_Rep2_ATH1") was made from "" 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: Civale_571-11_Hypoxia-24hrs-nia1_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.424141
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-ratio1.220583
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.908709
Spike_AFFX-r2-Bs-dap_5_signal36.061363
NoiseAvg:2.63,Std:0.11,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_signal12.966395
#P15567
Spike_AFFX-r2-Bs-phe_M_signal15.886675
Corner-Avg:9741,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.540260
Spike_AFFX-r2-Ec-bioB_3_signal43.392109
Spike_AFFX-r2-Bs-lys_M_signal16.295650
Spike_AFFX-r2-P1-cre_3_signal3315.786377
Spike_AFFX-r2-Bs-lys_3-5-ratio1.377234
Spike_AFFX-r2-Bs-dap_M_signal88.548409
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.674359
Spike_AFFX-r2-Ec-bioB_avg-signal59.227909
Spike_AFFX-r2-Bs-thr_avg-signal35.999165
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal463.632355
Spike_AFFX-r2-Bs-phe_5_signal14.920278
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal819.601501
RawQ2.475571
Spike_AFFX-r2-Bs-lys_5_signal12.786146
Signal(A)2.497062
%A30.469093
Signal(All)136.691574
Corner+Avg:154,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal182.726059
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.418734
Spike_AFFX-r2-Ec-bioD_avg-signal641.616943
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.246384
Spike_AFFX-r2-Bs-lys_avg-signal15.563771
Spike_AFFX-r2-P1-cre_avg-signal3016.173340
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.284524
Spike_AFFX-r2-Bs-thr_3_signal60.609592
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.741896
Spike_AFFX-r2-Bs-dap_3_signal149.711273
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.767783
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal167.553329
#M293
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.609516
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.090555
Spike_AFFX-r2-Bs-thr_M_signal34.421501
Signal(P)198.989197
Spike_AFFX-r2-Bs-phe_3-5-ratio1.904705
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7628,Count:9
Spike_AFFX-r2-P1-cre_5_signal2716.560303
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6950
Signal(M)9.950426
BackgroundAvg:57.60,Std:1.10,Min:54.8,Max:61.1
Spike_AFFX-r2-Ec-bioC_avg-signal175.139694
Spike_AFFX-r2-Bs-dap_avg-signal91.440346
Spike_AFFX-r2-Bs-dap_3-5-ratio4.151570
Spike_AFFX-r2-Ec-bioB_5_signal47.751362
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.424141
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-12_Hypoxia-24hrs-nia1_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 ("Civale_571-12_Hypoxia-24hrs-nia1_Rep3_ATH1") was made from "" 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: Civale_571-12_Hypoxia-24hrs-nia1_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.634576
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-ratio1.233135
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.985270
Spike_AFFX-r2-Bs-dap_5_signal44.091602
NoiseAvg:2.70,Std:0.35,Min:2.2,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.728184
#P15053
Spike_AFFX-r2-Bs-phe_M_signal18.126352
Corner-Avg:9894,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.274750
Spike_AFFX-r2-Ec-bioB_3_signal55.462379
Spike_AFFX-r2-Bs-lys_M_signal13.788489
Spike_AFFX-r2-P1-cre_3_signal3595.990723
Spike_AFFX-r2-Bs-lys_3-5-ratio3.066295
Spike_AFFX-r2-Bs-dap_M_signal78.814957
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.912939
Spike_AFFX-r2-Ec-bioB_avg-signal66.676231
Spike_AFFX-r2-Bs-thr_avg-signal35.441456
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal572.448425
Spike_AFFX-r2-Bs-phe_5_signal23.594873
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal894.548096
RawQ2.437886
Spike_AFFX-r2-Bs-lys_5_signal10.235951
Signal(A)3.477724
%A32.437527
Signal(All)139.220734
Corner+Avg:150,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal204.041489
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.359598
Spike_AFFX-r2-Ec-bioD_avg-signal733.498291
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.992989
Spike_AFFX-r2-Bs-lys_avg-signal18.470297
Spike_AFFX-r2-P1-cre_avg-signal3256.063477
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.569487
Spike_AFFX-r2-Bs-thr_3_signal57.630486
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-signal22.693609
Spike_AFFX-r2-Bs-dap_3_signal129.082184
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.562670
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal179.549759
#M358
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.386448
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.136406
Spike_AFFX-r2-Bs-thr_M_signal33.965702
Signal(P)208.942566
Spike_AFFX-r2-Bs-phe_3-5-ratio1.117175
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7485,Count:9
Spike_AFFX-r2-P1-cre_5_signal2916.136475
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7399
Signal(M)13.075091
BackgroundAvg:54.23,Std:0.80,Min:52.3,Max:57.0
Spike_AFFX-r2-Ec-bioC_avg-signal191.795624
Spike_AFFX-r2-Bs-dap_avg-signal83.996246
Spike_AFFX-r2-Bs-dap_3-5-ratio2.927591
Spike_AFFX-r2-Ec-bioB_5_signal56.291576
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.634576
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-13_Leaf-40-days_1239_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 ("Civale_571-13_Leaf-40-days_1239_Rep1_ATH1") was made from "" 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: Civale_571-13_Leaf-40-days_1239_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.424304
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-ratio1.249650
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.203124
Spike_AFFX-r2-Bs-dap_5_signal52.590519
NoiseAvg:2.64,Std:0.05,Min:2.4,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_signal33.546940
#P13964
Spike_AFFX-r2-Bs-phe_M_signal29.650997
Corner-Avg:11520,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal114.131714
Spike_AFFX-r2-Ec-bioB_3_signal84.303505
Spike_AFFX-r2-Bs-lys_M_signal7.828766
Spike_AFFX-r2-P1-cre_3_signal4902.630859
Spike_AFFX-r2-Bs-lys_3-5-ratio2.359628
Spike_AFFX-r2-Bs-dap_M_signal192.626556
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.834680
Spike_AFFX-r2-Ec-bioB_avg-signal89.501900
Spike_AFFX-r2-Bs-thr_avg-signal49.391388
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal746.844788
Spike_AFFX-r2-Bs-phe_5_signal30.100315
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1479.842896
RawQ2.429923
Spike_AFFX-r2-Bs-lys_5_signal17.218740
Signal(A)2.998341
%A37.198597
Signal(All)150.198029
Corner+Avg:181,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal296.708466
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.933319
Spike_AFFX-r2-Ec-bioD_avg-signal1113.343872
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.218765
Spike_AFFX-r2-Bs-lys_avg-signal21.892447
Spike_AFFX-r2-P1-cre_avg-signal4412.916504
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.582639
Spike_AFFX-r2-Bs-thr_3_signal61.547894
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.228210
Spike_AFFX-r2-Bs-dap_3_signal201.610138
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.981460
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal299.403198
#M361
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.629829
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.991000
Spike_AFFX-r2-Bs-thr_M_signal53.079334
Signal(P)243.198380
Spike_AFFX-r2-Bs-phe_3-5-ratio1.127341
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9548,Count:9
Spike_AFFX-r2-P1-cre_5_signal3923.201904
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8485
Signal(M)12.614838
BackgroundAvg:59.19,Std:0.48,Min:57.8,Max:60.5
Spike_AFFX-r2-Ec-bioC_avg-signal298.055847
Spike_AFFX-r2-Bs-dap_avg-signal148.942398
Spike_AFFX-r2-Bs-dap_3-5-ratio3.833583
Spike_AFFX-r2-Ec-bioB_5_signal70.070496
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.424304
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-14_Leaf-40-days_1239_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 ("Civale_571-14_Leaf-40-days_1239_Rep2_ATH1") was made from "" 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: Civale_571-14_Leaf-40-days_1239_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.581672
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-ratio1.123520
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.082297
Spike_AFFX-r2-Bs-dap_5_signal47.528519
NoiseAvg:2.38,Std:0.07,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_signal25.283642
#P13682
Spike_AFFX-r2-Bs-phe_M_signal30.187107
Corner-Avg:10703,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.859497
Spike_AFFX-r2-Ec-bioB_3_signal89.561005
Spike_AFFX-r2-Bs-lys_M_signal10.569270
Spike_AFFX-r2-P1-cre_3_signal4490.851563
Spike_AFFX-r2-Bs-lys_3-5-ratio1.764888
Spike_AFFX-r2-Bs-dap_M_signal121.803024
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.079770
Spike_AFFX-r2-Ec-bioB_avg-signal99.057106
Spike_AFFX-r2-Bs-thr_avg-signal41.564587
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal698.931824
Spike_AFFX-r2-Bs-phe_5_signal24.470402
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1369.805054
RawQ2.326608
Spike_AFFX-r2-Bs-lys_5_signal13.961484
Signal(A)3.276219
%A38.281456
Signal(All)152.893524
Corner+Avg:171,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal312.702026
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.176134
Spike_AFFX-r2-Ec-bioD_avg-signal1034.368408
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.982464
Spike_AFFX-r2-Bs-lys_avg-signal16.390404
Spike_AFFX-r2-P1-cre_avg-signal4243.988770
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.736081
Spike_AFFX-r2-Bs-thr_3_signal52.584148
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal28.277884
Spike_AFFX-r2-Bs-dap_3_signal133.238037
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.959855
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal325.847046
#M396
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.640457
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.959659
Spike_AFFX-r2-Bs-thr_M_signal46.825962
Signal(P)252.422165
Spike_AFFX-r2-Bs-phe_3-5-ratio1.233169
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8985,Count:9
Spike_AFFX-r2-P1-cre_5_signal3997.125977
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8732
Signal(M)13.265815
BackgroundAvg:55.25,Std:0.44,Min:54.4,Max:57.0
Spike_AFFX-r2-Ec-bioC_avg-signal319.274536
Spike_AFFX-r2-Bs-dap_avg-signal100.856529
Spike_AFFX-r2-Bs-dap_3-5-ratio2.803328
Spike_AFFX-r2-Ec-bioB_5_signal82.750824
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.581672
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-15_Leaf-40-days_1239_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 ("Civale_571-15_Leaf-40-days_1239_Rep3_ATH1") was made from "" 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: Civale_571-15_Leaf-40-days_1239_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.588671
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-ratio1.147264
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.587040
Spike_AFFX-r2-Bs-dap_5_signal45.256683
NoiseAvg:2.41,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_signal28.273407
#P13513
Spike_AFFX-r2-Bs-phe_M_signal27.836920
Corner-Avg:10898,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal113.715347
Spike_AFFX-r2-Ec-bioB_3_signal100.692390
Spike_AFFX-r2-Bs-lys_M_signal9.122694
Spike_AFFX-r2-P1-cre_3_signal4804.542969
Spike_AFFX-r2-Bs-lys_3-5-ratio2.819802
Spike_AFFX-r2-Bs-dap_M_signal148.638092
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.005662
Spike_AFFX-r2-Ec-bioB_avg-signal92.618134
Spike_AFFX-r2-Bs-thr_avg-signal45.859074
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal850.592590
Spike_AFFX-r2-Bs-phe_5_signal23.564077
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1535.424683
RawQ2.376239
Spike_AFFX-r2-Bs-lys_5_signal12.569229
Signal(A)3.737081
%A38.877686
Signal(All)152.051010
Corner+Avg:168,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal287.608185
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.494419
Spike_AFFX-r2-Ec-bioD_avg-signal1193.008667
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.241562
Spike_AFFX-r2-Bs-lys_avg-signal19.044886
Spike_AFFX-r2-P1-cre_avg-signal4496.185059
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_signal56.706894
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal28.631805
Spike_AFFX-r2-Bs-dap_3_signal160.306458
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.805124
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal345.895752
#M429
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.442734
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.831488
Spike_AFFX-r2-Bs-thr_M_signal52.596920
Signal(P)253.732330
Spike_AFFX-r2-Bs-phe_3-5-ratio1.463856
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7969,Count:9
Spike_AFFX-r2-P1-cre_5_signal4187.827148
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8868
Signal(M)15.053763
BackgroundAvg:54.66,Std:0.57,Min:53.3,Max:56.1
Spike_AFFX-r2-Ec-bioC_avg-signal316.751953
Spike_AFFX-r2-Bs-dap_avg-signal118.067078
Spike_AFFX-r2-Bs-dap_3-5-ratio3.542161
Spike_AFFX-r2-Ec-bioB_5_signal63.446663
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.588671
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-16_Mersitem-40-days_1239_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Civale_571-16_Mersitem-40-days_1239_Rep1_ATH1") was made from "" 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: Civale_571-16_Mersitem-40-days_1239_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.362035
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-ratio1.146795
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.944485
Spike_AFFX-r2-Bs-dap_5_signal45.272472
NoiseAvg:2.61,Std:0.08,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_signal22.315538
#P15289
Spike_AFFX-r2-Bs-phe_M_signal27.455498
Corner-Avg:14815,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal98.458794
Spike_AFFX-r2-Ec-bioB_3_signal82.189888
Spike_AFFX-r2-Bs-lys_M_signal11.752513
Spike_AFFX-r2-P1-cre_3_signal3798.976807
Spike_AFFX-r2-Bs-lys_3-5-ratio2.246118
Spike_AFFX-r2-Bs-dap_M_signal161.896912
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.926253
Spike_AFFX-r2-Ec-bioB_avg-signal89.223167
Spike_AFFX-r2-Bs-thr_avg-signal55.037045
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal637.016113
Spike_AFFX-r2-Bs-phe_5_signal25.795483
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1051.221436
RawQ2.354498
Spike_AFFX-r2-Bs-lys_5_signal17.337091
Signal(A)2.292004
%A31.696625
Signal(All)137.939148
Corner+Avg:253,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal263.998260
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.587797
Spike_AFFX-r2-Ec-bioD_avg-signal844.118774
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.027618
Spike_AFFX-r2-Bs-lys_avg-signal22.676920
Spike_AFFX-r2-P1-cre_avg-signal3555.834229
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.275756
Spike_AFFX-r2-Bs-thr_3_signal87.616447
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.946259
Spike_AFFX-r2-Bs-dap_3_signal228.060623
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.650227
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.111206
#M291
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.941154
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.022808
Spike_AFFX-r2-Bs-thr_M_signal55.179153
Signal(P)204.527542
Spike_AFFX-r2-Bs-phe_3-5-ratio1.069482
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12020,Count:9
Spike_AFFX-r2-P1-cre_5_signal3312.691650
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7230
Signal(M)9.619043
BackgroundAvg:53.06,Std:0.42,Min:52.2,Max:54.1
Spike_AFFX-r2-Ec-bioC_avg-signal261.054749
Spike_AFFX-r2-Bs-dap_avg-signal145.076660
Spike_AFFX-r2-Bs-dap_3-5-ratio5.037512
Spike_AFFX-r2-Ec-bioB_5_signal87.020805
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.362035
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-17_Mersitem-40-days_1239_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 ("Civale_571-17_Mersitem-40-days_1239_Rep2_ATH1") was made from "" 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: Civale_571-17_Mersitem-40-days_1239_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.536695
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-ratio1.026837
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.026719
Spike_AFFX-r2-Bs-dap_5_signal84.881088
NoiseAvg:2.31,Std:0.07,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_signal33.935711
#P15004
Spike_AFFX-r2-Bs-phe_M_signal35.001163
Corner-Avg:12497,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal147.281113
Spike_AFFX-r2-Ec-bioB_3_signal106.902809
Spike_AFFX-r2-Bs-lys_M_signal23.737049
Spike_AFFX-r2-P1-cre_3_signal4018.896240
Spike_AFFX-r2-Bs-lys_3-5-ratio1.178267
Spike_AFFX-r2-Bs-dap_M_signal252.695023
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.543564
Spike_AFFX-r2-Ec-bioB_avg-signal119.434914
Spike_AFFX-r2-Bs-thr_avg-signal80.119614
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal779.908142
Spike_AFFX-r2-Bs-phe_5_signal41.526314
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1290.299438
RawQ2.303339
Spike_AFFX-r2-Bs-lys_5_signal27.186148
Signal(A)2.780154
%A33.077599
Signal(All)141.331635
Corner+Avg:195,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal325.755676
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal55.057190
Spike_AFFX-r2-Ec-bioD_avg-signal1035.103760
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.778168
Spike_AFFX-r2-Bs-lys_avg-signal27.651915
Spike_AFFX-r2-P1-cre_avg-signal3966.378418
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.144235
Spike_AFFX-r2-Bs-thr_3_signal120.253357
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-signal43.861553
Spike_AFFX-r2-Bs-dap_3_signal300.042023
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.654425
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal409.475403
#M261
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.032543
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.795544
Spike_AFFX-r2-Bs-thr_M_signal86.169762
Signal(P)213.262375
Spike_AFFX-r2-Bs-phe_3-5-ratio1.325839
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10381,Count:9
Spike_AFFX-r2-P1-cre_5_signal3913.860352
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7545
Signal(M)11.531311
BackgroundAvg:53.90,Std:0.38,Min:53.2,Max:55.4
Spike_AFFX-r2-Ec-bioC_avg-signal367.615540
Spike_AFFX-r2-Bs-dap_avg-signal212.539383
Spike_AFFX-r2-Bs-dap_3-5-ratio3.534851
Spike_AFFX-r2-Ec-bioB_5_signal104.120827
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.536695
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-18_Mersitem-40-days_1239_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 ("Civale_571-18_Mersitem-40-days_1239_Rep3_ATH1") was made from "" 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: Civale_571-18_Mersitem-40-days_1239_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.42825
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-ratio1.104186
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.876933
Spike_AFFX-r2-Bs-dap_5_signal83.199036
NoiseAvg:2.54,Std:0.10,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_signal36.897964
#P15148
Spike_AFFX-r2-Bs-phe_M_signal37.662804
Corner-Avg:11468,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal118.698296
Spike_AFFX-r2-Ec-bioB_3_signal82.886383
Spike_AFFX-r2-Bs-lys_M_signal22.612728
Spike_AFFX-r2-P1-cre_3_signal4117.395020
Spike_AFFX-r2-Bs-lys_3-5-ratio1.458234
Spike_AFFX-r2-Bs-dap_M_signal237.293030
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.546887
Spike_AFFX-r2-Ec-bioB_avg-signal98.701042
Spike_AFFX-r2-Bs-thr_avg-signal97.238564
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal701.489258
Spike_AFFX-r2-Bs-phe_5_signal42.195786
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1252.940796
RawQ2.500420
Spike_AFFX-r2-Bs-lys_5_signal21.968750
Signal(A)2.223269
%A32.354229
Signal(All)140.269470
Corner+Avg:186,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal316.926941
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal45.491348
Spike_AFFX-r2-Ec-bioD_avg-signal977.215027
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.409470
Spike_AFFX-r2-Bs-lys_avg-signal25.539017
Spike_AFFX-r2-P1-cre_avg-signal3923.145020
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.236300
Spike_AFFX-r2-Bs-thr_3_signal167.770889
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-signal41.783314
Spike_AFFX-r2-Bs-dap_3_signal264.826324
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.786115
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal350.388214
#M282
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.035572
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.904502
Spike_AFFX-r2-Bs-thr_M_signal87.046867
Signal(P)209.928513
Spike_AFFX-r2-Bs-phe_3-5-ratio1.078102
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8352,Count:9
Spike_AFFX-r2-P1-cre_5_signal3728.895264
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7380
Signal(M)11.141476
BackgroundAvg:60.31,Std:0.62,Min:58.8,Max:62.1
Spike_AFFX-r2-Ec-bioC_avg-signal333.657593
Spike_AFFX-r2-Bs-dap_avg-signal195.106125
Spike_AFFX-r2-Bs-dap_3-5-ratio3.183046
Spike_AFFX-r2-Ec-bioB_5_signal94.518440
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.428250
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-19_Leaf-40-days_Col-0_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Civale_571-19_Leaf-40-days_Col-0_Rep1_ATH1") was made from "" 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: Civale_571-19_Leaf-40-days_Col-0_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.590466
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-ratio1.312673
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.371181
Spike_AFFX-r2-Bs-dap_5_signal45.452469
NoiseAvg:2.40,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_signal18.794516
#P13928
Spike_AFFX-r2-Bs-phe_M_signal26.063908
Corner-Avg:12475,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal134.251236
Spike_AFFX-r2-Ec-bioB_3_signal125.407112
Spike_AFFX-r2-Bs-lys_M_signal15.313549
Spike_AFFX-r2-P1-cre_3_signal5385.982422
Spike_AFFX-r2-Bs-lys_3-5-ratio2.561667
Spike_AFFX-r2-Bs-dap_M_signal136.553223
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.754512
Spike_AFFX-r2-Ec-bioB_avg-signal117.039192
Spike_AFFX-r2-Bs-thr_avg-signal35.453835
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal894.952332
Spike_AFFX-r2-Bs-phe_5_signal23.753597
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1654.414917
RawQ2.409770
Spike_AFFX-r2-Bs-lys_5_signal14.526952
Signal(A)3.307640
%A37.299431
Signal(All)150.954819
Corner+Avg:197,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal320.657684
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.379967
Spike_AFFX-r2-Ec-bioD_avg-signal1274.683594
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.060940
Spike_AFFX-r2-Bs-lys_avg-signal22.351236
Spike_AFFX-r2-P1-cre_avg-signal4744.523926
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_signal51.769722
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal28.065825
Spike_AFFX-r2-Bs-dap_3_signal165.159271
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.848607
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal358.652924
#M374
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.213211
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.894061
Spike_AFFX-r2-Bs-thr_M_signal35.797268
Signal(P)244.843002
Spike_AFFX-r2-Bs-phe_3-5-ratio1.447358
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10489,Count:9
Spike_AFFX-r2-P1-cre_5_signal4103.065430
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8508
Signal(M)13.274924
BackgroundAvg:55.52,Std:0.30,Min:55.1,Max:56.7
Spike_AFFX-r2-Ec-bioC_avg-signal339.655304
Spike_AFFX-r2-Bs-dap_avg-signal115.721657
Spike_AFFX-r2-Bs-dap_3-5-ratio3.633670
Spike_AFFX-r2-Ec-bioB_5_signal91.459221
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.590466
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-20_Leaf-40-days_Col-0_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-20_Leaf-40-days_Col-0_Rep2_ATH1") was made from "" 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: Civale_571-20_Leaf-40-days_Col-0_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.856986
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-ratio1.101820
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.316652
Spike_AFFX-r2-Bs-dap_5_signal38.100155
NoiseAvg:2.41,Std:0.05,Min:2.3,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_signal31.369255
#P13243
Spike_AFFX-r2-Bs-phe_M_signal38.988617
Corner-Avg:9809,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal131.002274
Spike_AFFX-r2-Ec-bioB_3_signal102.461838
Spike_AFFX-r2-Bs-lys_M_signal9.363870
Spike_AFFX-r2-P1-cre_3_signal5192.470215
Spike_AFFX-r2-Bs-lys_3-5-ratio2.614406
Spike_AFFX-r2-Bs-dap_M_signal153.539719
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.146486
Spike_AFFX-r2-Ec-bioB_avg-signal103.761353
Spike_AFFX-r2-Bs-thr_avg-signal66.228752
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal849.099548
Spike_AFFX-r2-Bs-phe_5_signal25.109262
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1708.227417
RawQ2.452723
Spike_AFFX-r2-Bs-lys_5_signal13.854756
Signal(A)4.604563
%A40.236740
Signal(All)154.448532
Corner+Avg:164,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal323.303986
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.469612
Spike_AFFX-r2-Ec-bioD_avg-signal1278.663452
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.057869
Spike_AFFX-r2-Bs-lys_avg-signal19.813528
Spike_AFFX-r2-P1-cre_avg-signal4952.551270
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal98.702911
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal32.522495
Spike_AFFX-r2-Bs-dap_3_signal178.453476
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.011811
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal400.175629
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.221962
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.807905
Spike_AFFX-r2-Bs-thr_M_signal68.614067
Signal(P)262.267700
Spike_AFFX-r2-Bs-phe_3-5-ratio1.332959
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7912,Count:9
Spike_AFFX-r2-P1-cre_5_signal4712.632324
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9178
Signal(M)19.278822
BackgroundAvg:57.72,Std:0.60,Min:56.5,Max:59.3
Spike_AFFX-r2-Ec-bioC_avg-signal361.739807
Spike_AFFX-r2-Bs-dap_avg-signal123.364449
Spike_AFFX-r2-Bs-dap_3-5-ratio4.683799
Spike_AFFX-r2-Ec-bioB_5_signal77.819962
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.856986
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-21_Leaf-40-days_Col-0_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-21_Leaf-40-days_Col-0_Rep3_ATH1") was made from "" 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: Civale_571-21_Leaf-40-days_Col-0_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.411341
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-ratio1.158134
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.282866
Spike_AFFX-r2-Bs-dap_5_signal45.585964
NoiseAvg:3.02,Std:0.08,Min:2.8,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_signal26.154772
#P13880
Spike_AFFX-r2-Bs-phe_M_signal27.802673
Corner-Avg:10938,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal101.000961
Spike_AFFX-r2-Ec-bioB_3_signal81.686928
Spike_AFFX-r2-Bs-lys_M_signal6.130359
Spike_AFFX-r2-P1-cre_3_signal3714.342773
Spike_AFFX-r2-Bs-lys_3-5-ratio1.559370
Spike_AFFX-r2-Bs-dap_M_signal164.135590
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.405965
Spike_AFFX-r2-Ec-bioB_avg-signal82.121071
Spike_AFFX-r2-Bs-thr_avg-signal47.276508
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal616.361206
Spike_AFFX-r2-Bs-phe_5_signal26.322458
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1243.811035
RawQ2.777759
Spike_AFFX-r2-Bs-lys_5_signal17.409933
Signal(A)3.353623
%A37.501095
Signal(All)147.938293
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal262.236206
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.997791
Spike_AFFX-r2-Ec-bioD_avg-signal930.086121
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.850506
Spike_AFFX-r2-Bs-lys_avg-signal16.896276
Spike_AFFX-r2-P1-cre_avg-signal3460.760254
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.648400
Spike_AFFX-r2-Bs-thr_3_signal62.927471
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.040976
Spike_AFFX-r2-Bs-dap_3_signal190.921570
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.017990
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal270.025665
#M376
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.148533
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.971153
Spike_AFFX-r2-Bs-thr_M_signal52.747280
Signal(P)240.709305
Spike_AFFX-r2-Bs-phe_3-5-ratio1.025656
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8423,Count:9
Spike_AFFX-r2-P1-cre_5_signal3207.177979
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8554
Signal(M)12.607301
BackgroundAvg:69.70,Std:0.48,Min:67.8,Max:70.7
Spike_AFFX-r2-Ec-bioC_avg-signal266.130920
Spike_AFFX-r2-Bs-dap_avg-signal133.547714
Spike_AFFX-r2-Bs-dap_3-5-ratio4.188166
Spike_AFFX-r2-Ec-bioB_5_signal63.675331
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.411341
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-22_Mersitem-40-days_Col-0_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Civale_571-22_Mersitem-40-days_Col-0_Rep1_ATH1") was made from "" 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: Civale_571-22_Mersitem-40-days_Col-0_Rep1_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.439255
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-ratio1.142733
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.818474
Spike_AFFX-r2-Bs-dap_5_signal56.315010
NoiseAvg:2.44,Std:0.06,Min:2.3,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_signal23.726208
#P15443
Spike_AFFX-r2-Bs-phe_M_signal20.950474
Corner-Avg:12248,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal112.777008
Spike_AFFX-r2-Ec-bioB_3_signal80.484688
Spike_AFFX-r2-Bs-lys_M_signal6.871386
Spike_AFFX-r2-P1-cre_3_signal4152.796875
Spike_AFFX-r2-Bs-lys_3-5-ratio1.775351
Spike_AFFX-r2-Bs-dap_M_signal137.310944
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.776209
Spike_AFFX-r2-Ec-bioB_avg-signal97.198936
Spike_AFFX-r2-Bs-thr_avg-signal44.225666
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal660.411133
Spike_AFFX-r2-Bs-phe_5_signal25.571869
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1090.796387
RawQ2.403715
Spike_AFFX-r2-Bs-lys_5_signal13.868813
Signal(A)2.168713
%A31.017097
Signal(All)138.520035
Corner+Avg:187,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal304.045807
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.575197
Spike_AFFX-r2-Ec-bioD_avg-signal875.603760
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.702759
Spike_AFFX-r2-Bs-lys_avg-signal15.120738
Spike_AFFX-r2-P1-cre_avg-signal3893.444092
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.280140
Spike_AFFX-r2-Bs-thr_3_signal65.868904
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-signal22.699181
Spike_AFFX-r2-Bs-dap_3_signal204.973877
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.651693
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal296.463104
#M292
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.622015
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.025577
Spike_AFFX-r2-Bs-thr_M_signal43.081890
Signal(P)203.418777
Spike_AFFX-r2-Bs-phe_3-5-ratio0.843708
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9702,Count:9
Spike_AFFX-r2-P1-cre_5_signal3634.091309
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7075
Signal(M)9.938803
BackgroundAvg:57.00,Std:0.61,Min:55.8,Max:58.8
Spike_AFFX-r2-Ec-bioC_avg-signal300.254456
Spike_AFFX-r2-Bs-dap_avg-signal132.866608
Spike_AFFX-r2-Bs-dap_3-5-ratio3.639773
Spike_AFFX-r2-Ec-bioB_5_signal98.335114
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.439255
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-23_Mersitem-40-days_Col-0_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-23_Mersitem-40-days_Col-0_Rep2_ATH1") was made from "" 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: Civale_571-23_Mersitem-40-days_Col-0_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.572915
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-ratio0.965851
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.116413
Spike_AFFX-r2-Bs-dap_5_signal122.115326
NoiseAvg:2.34,Std:0.10,Min:2.0,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_signal32.597874
#P15257
Spike_AFFX-r2-Bs-phe_M_signal32.450470
Corner-Avg:11765,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal122.582878
Spike_AFFX-r2-Ec-bioB_3_signal90.972839
Spike_AFFX-r2-Bs-lys_M_signal19.027134
Spike_AFFX-r2-P1-cre_3_signal3977.537842
Spike_AFFX-r2-Bs-lys_3-5-ratio1.438093
Spike_AFFX-r2-Bs-dap_M_signal220.383850
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.336559
Spike_AFFX-r2-Ec-bioB_avg-signal98.347481
Spike_AFFX-r2-Bs-thr_avg-signal98.222832
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal814.897705
Spike_AFFX-r2-Bs-phe_5_signal44.716618
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1141.710938
RawQ2.425055
Spike_AFFX-r2-Bs-lys_5_signal25.862507
Signal(A)2.838115
%A31.845682
Signal(All)140.282684
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal322.961334
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.803303
Spike_AFFX-r2-Ec-bioD_avg-signal978.304321
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.887329
Spike_AFFX-r2-Bs-lys_avg-signal27.360773
Spike_AFFX-r2-P1-cre_avg-signal4047.853027
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.266988
Spike_AFFX-r2-Bs-thr_3_signal173.960464
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-signal43.323460
Spike_AFFX-r2-Bs-dap_3_signal327.471100
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.401048
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal273.584106
#M289
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.192680
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.180483
Spike_AFFX-r2-Bs-thr_M_signal88.110168
Signal(P)208.148788
Spike_AFFX-r2-Bs-phe_3-5-ratio1.180843
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9605,Count:9
Spike_AFFX-r2-P1-cre_5_signal4118.167969
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7264
Signal(M)12.130866
BackgroundAvg:55.12,Std:0.81,Min:53.2,Max:56.8
Spike_AFFX-r2-Ec-bioC_avg-signal298.272705
Spike_AFFX-r2-Bs-dap_avg-signal223.323441
Spike_AFFX-r2-Bs-dap_3-5-ratio2.681654
Spike_AFFX-r2-Ec-bioB_5_signal81.486732
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.572915
NF1.000000
HZ4
Tau0.015000

Slide: Civale_571-24_Mersitem-40-days_Col-0_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Civale_571-24_Mersitem-40-days_Col-0_Rep3_ATH1") was made from "" 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: Civale_571-24_Mersitem-40-days_Col-0_Rep3_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.593984
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-ratio1.116403
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.879688
Spike_AFFX-r2-Bs-dap_5_signal44.019287
NoiseAvg:2.40,Std:0.11,Min:2.1,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_signal19.738127
#P15081
Spike_AFFX-r2-Bs-phe_M_signal20.148161
Corner-Avg:9848,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal97.974609
Spike_AFFX-r2-Ec-bioB_3_signal80.590355
Spike_AFFX-r2-Bs-lys_M_signal14.220134
Spike_AFFX-r2-P1-cre_3_signal4725.505859
Spike_AFFX-r2-Bs-lys_3-5-ratio1.271428
Spike_AFFX-r2-Bs-dap_M_signal172.491989
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.834392
Spike_AFFX-r2-Ec-bioB_avg-signal90.059143
Spike_AFFX-r2-Bs-thr_avg-signal67.409248
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal753.872192
Spike_AFFX-r2-Bs-phe_5_signal26.969311
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1219.583984
RawQ2.494147
Spike_AFFX-r2-Bs-lys_5_signal22.665810
Signal(A)2.905499
%A32.665497
Signal(All)141.448761
Corner+Avg:155,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal330.390778
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.648052
Spike_AFFX-r2-Ec-bioD_avg-signal986.728088
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.115738
Spike_AFFX-r2-Bs-lys_avg-signal21.901299
Spike_AFFX-r2-P1-cre_avg-signal4479.151367
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.218764
Spike_AFFX-r2-Bs-thr_3_signal115.159973
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.921839
Spike_AFFX-r2-Bs-dap_3_signal199.494537
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.617760
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal320.988953
#M278
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.817953
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.029290
Spike_AFFX-r2-Bs-thr_M_signal67.329659
Signal(P)212.289444
Spike_AFFX-r2-Bs-phe_3-5-ratio1.247642
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6907,Count:9
Spike_AFFX-r2-P1-cre_5_signal4232.797363
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7451
Signal(M)11.727965
BackgroundAvg:58.36,Std:0.55,Min:57.1,Max:60.0
Spike_AFFX-r2-Ec-bioC_avg-signal325.689880
Spike_AFFX-r2-Bs-dap_avg-signal138.668594
Spike_AFFX-r2-Bs-dap_3-5-ratio4.531980
Spike_AFFX-r2-Ec-bioB_5_signal91.612457
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.593984
NF1.000000
HZ4
Tau0.015000


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