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Experiment: Jasmonate Continuous Growth Control

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-568

Aim: to establish the link between jasmonate signalling and growth controlGenotypes analysed: coi1-16 and aos vs Col-gl1Tissue: first leaf pairsTime point: 9, 13 and 19 days after sowingTreatment: Continuous growth on MS medium +/- MeJA [50uM], long day conditions, 22 degrees

About the Experimenter

Name:Dr Sandra Noir
Head of Lab Name:Dr Alessandra Devoto
Lab:
Address:Department of Biological Sciences, Faculty of Science, Royal Holloway, University of London
Bourne Laboratory, Egham Hill, Egham, Surrey
Postcode: TW20 0EX
Country: UNITED KINGDOM
 
Telephone Number: +44 (0)1784-41-4389
Fax Number: +44 (0)1784-41-4224

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: compound_based_treatment
Number of Slides:14
 
Experimental Parameters:
parameter compound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Noir: Jasmonate Continuous Growth Control

Slide: Noir_568-1_1/9-gl+_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 ("Noir_568-1_1/9-gl+_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: Noir_568-1_1/9-gl+_Rep1_ATH1
Organism:
Alias: Col-gl1
Stock Code:
Age: 9 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium + [50uM] MeJA, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.833668
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-ratio1.249760
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.254321
Spike_AFFX-r2-Bs-dap_5_signal132.611343
NoiseAvg:2.09,Std:0.08,Min:1.9,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal64.960182
#P13802
Spike_AFFX-r2-Bs-phe_M_signal41.728416
Corner-Avg:8532,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal160.601318
Spike_AFFX-r2-Ec-bioB_3_signal104.018051
Spike_AFFX-r2-Bs-lys_M_signal17.367277
Spike_AFFX-r2-P1-cre_3_signal7469.415039
Spike_AFFX-r2-Bs-lys_3-5-ratio1.944486
Spike_AFFX-r2-Bs-dap_M_signal303.243439
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.673095
Spike_AFFX-r2-Ec-bioB_avg-signal115.849052
Spike_AFFX-r2-Bs-thr_avg-signal89.743744
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1112.305420
Spike_AFFX-r2-Bs-phe_5_signal42.293514
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1857.134033
RawQ2.135875
Spike_AFFX-r2-Bs-lys_5_signal26.977440
Signal(A)4.720059
%A37.786060
Signal(All)153.649338
Corner+Avg:139,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal391.980652
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal55.471333
Spike_AFFX-r2-Ec-bioD_avg-signal1484.719727
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.508549
Spike_AFFX-r2-Bs-lys_avg-signal32.267323
Spike_AFFX-r2-P1-cre_avg-signal6723.046875
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal108.684555
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-signal46.497757
Spike_AFFX-r2-Bs-dap_3_signal299.088654
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.669626
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal372.576935
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal52.457249
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.052080
Spike_AFFX-r2-Bs-thr_M_signal95.586510
Signal(P)250.438492
Spike_AFFX-r2-Bs-phe_3-5-ratio1.311580
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6237,Count:9
Spike_AFFX-r2-P1-cre_5_signal5976.678223
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8619
Signal(M)19.298765
BackgroundAvg:47.38,Std:0.34,Min:46.5,Max:48.4
Spike_AFFX-r2-Ec-bioC_avg-signal382.278809
Spike_AFFX-r2-Bs-dap_avg-signal244.981140
Spike_AFFX-r2-Bs-dap_3-5-ratio2.255378
Spike_AFFX-r2-Ec-bioB_5_signal82.927773
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.833668
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-2_1/9-gl-_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 ("Noir_568-2_1/9-gl-_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: Noir_568-2_1/9-gl-_Rep1_ATH1
Organism:
Alias: Col-gl1
Stock Code:
Age: 9 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.639911
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-ratio1.203705
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.299502
Spike_AFFX-r2-Bs-dap_5_signal154.743332
NoiseAvg:2.50,Std:0.05,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_signal55.682762
#P13786
Spike_AFFX-r2-Bs-phe_M_signal31.277149
Corner-Avg:11058,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal127.265717
Spike_AFFX-r2-Ec-bioB_3_signal111.476517
Spike_AFFX-r2-Bs-lys_M_signal18.379442
Spike_AFFX-r2-P1-cre_3_signal6918.606934
Spike_AFFX-r2-Bs-lys_3-5-ratio1.602193
Spike_AFFX-r2-Bs-dap_M_signal271.842529
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.034197
Spike_AFFX-r2-Ec-bioB_avg-signal108.175423
Spike_AFFX-r2-Bs-thr_avg-signal84.754890
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1340.564941
Spike_AFFX-r2-Bs-phe_5_signal44.070232
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2072.711670
RawQ2.446330
Spike_AFFX-r2-Bs-lys_5_signal31.076838
Signal(A)4.005179
%A37.930733
Signal(All)159.296387
Corner+Avg:178,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal387.416718
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.984695
Spike_AFFX-r2-Ec-bioD_avg-signal1706.638306
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.438404
Spike_AFFX-r2-Bs-lys_avg-signal33.082451
Spike_AFFX-r2-P1-cre_avg-signal6333.183594
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.630864
Spike_AFFX-r2-Bs-thr_3_signal113.269707
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal40.777359
Spike_AFFX-r2-Bs-dap_3_signal388.737610
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.546148
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal388.351563
#M372
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.791077
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.997593
Spike_AFFX-r2-Bs-thr_M_signal85.312210
Signal(P)260.586151
Spike_AFFX-r2-Bs-phe_3-5-ratio1.066132
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7683,Count:9
Spike_AFFX-r2-P1-cre_5_signal5747.760254
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8652
Signal(M)17.358027
BackgroundAvg:54.95,Std:0.27,Min:54.2,Max:55.9
Spike_AFFX-r2-Ec-bioC_avg-signal387.884155
Spike_AFFX-r2-Bs-dap_avg-signal271.774506
Spike_AFFX-r2-Bs-dap_3-5-ratio2.512145
Spike_AFFX-r2-Ec-bioB_5_signal85.784035
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.639911
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-3_1/9-coi1+_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 ("Noir_568-3_1/9-coi1+_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: Noir_568-3_1/9-coi1+_Rep1_ATH1
Organism:
Alias: coi1-16
Stock Code:
Age: 9 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium + [50uM] MeJA, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.712728
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-ratio1.175400
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.385561
Spike_AFFX-r2-Bs-dap_5_signal81.352890
NoiseAvg:2.60,Std:0.07,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_signal42.966652
#P13691
Spike_AFFX-r2-Bs-phe_M_signal39.691257
Corner-Avg:10065,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal112.053902
Spike_AFFX-r2-Ec-bioB_3_signal84.191521
Spike_AFFX-r2-Bs-lys_M_signal10.068254
Spike_AFFX-r2-P1-cre_3_signal5962.984863
Spike_AFFX-r2-Bs-lys_3-5-ratio1.607455
Spike_AFFX-r2-Bs-dap_M_signal206.471893
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.038356
Spike_AFFX-r2-Ec-bioB_avg-signal85.669640
Spike_AFFX-r2-Bs-thr_avg-signal64.822502
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal850.593994
Spike_AFFX-r2-Bs-phe_5_signal37.865639
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1597.777466
RawQ2.621998
Spike_AFFX-r2-Bs-lys_5_signal19.879965
Signal(A)4.746345
%A38.263920
Signal(All)154.290878
Corner+Avg:161,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal282.403717
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.200802
Spike_AFFX-r2-Ec-bioD_avg-signal1224.185791
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.021919
Spike_AFFX-r2-Bs-lys_avg-signal20.634790
Spike_AFFX-r2-P1-cre_avg-signal5518.070313
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.714160
Spike_AFFX-r2-Bs-thr_3_signal87.581345
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-signal41.252567
Spike_AFFX-r2-Bs-dap_3_signal281.250519
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.878425
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal316.647217
#M391
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.956156
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.891856
Spike_AFFX-r2-Bs-thr_M_signal63.919495
Signal(P)253.518600
Spike_AFFX-r2-Bs-phe_3-5-ratio1.220125
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6589,Count:9
Spike_AFFX-r2-P1-cre_5_signal5073.155273
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8728
Signal(M)17.968704
BackgroundAvg:61.19,Std:0.30,Min:60.4,Max:62.1
Spike_AFFX-r2-Ec-bioC_avg-signal299.525452
Spike_AFFX-r2-Bs-dap_avg-signal189.691772
Spike_AFFX-r2-Bs-dap_3-5-ratio3.457167
Spike_AFFX-r2-Ec-bioB_5_signal60.763496
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.712728
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-4_1/9-coi1-_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 ("Noir_568-4_1/9-coi1-_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: Noir_568-4_1/9-coi1-_Rep1_ATH1
Organism:
Alias: coi1-16
Stock Code:
Age: 9 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.702112
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-ratio1.384402
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.599615
Spike_AFFX-r2-Bs-dap_5_signal129.039261
NoiseAvg:2.79,Std:0.09,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal43.601986
#P13401
Spike_AFFX-r2-Bs-phe_M_signal37.310726
Corner-Avg:17283,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal120.318733
Spike_AFFX-r2-Ec-bioB_3_signal90.669731
Spike_AFFX-r2-Bs-lys_M_signal14.886705
Spike_AFFX-r2-P1-cre_3_signal6717.937988
Spike_AFFX-r2-Bs-lys_3-5-ratio2.211972
Spike_AFFX-r2-Bs-dap_M_signal245.971283
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.691920
Spike_AFFX-r2-Ec-bioB_avg-signal89.223564
Spike_AFFX-r2-Bs-thr_avg-signal63.461514
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1158.222534
Spike_AFFX-r2-Bs-phe_5_signal45.099880
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1646.678467
RawQ2.627702
Spike_AFFX-r2-Bs-lys_5_signal22.612883
Signal(A)5.333344
%A39.395000
Signal(All)160.673218
Corner+Avg:294,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal246.593018
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.700439
Spike_AFFX-r2-Ec-bioD_avg-signal1402.450439
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.750549
Spike_AFFX-r2-Bs-lys_avg-signal29.172880
Spike_AFFX-r2-P1-cre_avg-signal5785.264648
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.854450
Spike_AFFX-r2-Bs-thr_3_signal73.771065
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.370350
Spike_AFFX-r2-Bs-dap_3_signal307.036530
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.421729
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal272.913330
#M423
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.019051
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.903558
Spike_AFFX-r2-Bs-thr_M_signal73.011482
Signal(P)269.295044
Spike_AFFX-r2-Bs-phe_3-5-ratio1.390257
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12884,Count:9
Spike_AFFX-r2-P1-cre_5_signal4852.591309
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8986
Signal(M)19.403158
BackgroundAvg:58.86,Std:0.45,Min:57.7,Max:59.8
Spike_AFFX-r2-Ec-bioC_avg-signal259.753174
Spike_AFFX-r2-Bs-dap_avg-signal227.349014
Spike_AFFX-r2-Bs-dap_3-5-ratio2.379404
Spike_AFFX-r2-Ec-bioB_5_signal56.682217
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.702112
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-5_1/13-gl+_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 ("Noir_568-5_1/13-gl+_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: Noir_568-5_1/13-gl+_Rep1_ATH1
Organism:
Alias: Col-gl1
Stock Code:
Age: 13 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium + [50uM] MeJA, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.813983
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-ratio1.266740
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.302062
Spike_AFFX-r2-Bs-dap_5_signal116.799187
NoiseAvg:2.49,Std:0.05,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_signal42.119583
#P13413
Spike_AFFX-r2-Bs-phe_M_signal40.378403
Corner-Avg:10977,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal131.755219
Spike_AFFX-r2-Ec-bioB_3_signal92.354919
Spike_AFFX-r2-Bs-lys_M_signal16.268282
Spike_AFFX-r2-P1-cre_3_signal6046.566406
Spike_AFFX-r2-Bs-lys_3-5-ratio1.513843
Spike_AFFX-r2-Bs-dap_M_signal209.154037
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.783049
Spike_AFFX-r2-Ec-bioB_avg-signal98.346619
Spike_AFFX-r2-Bs-thr_avg-signal75.625999
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal967.310730
Spike_AFFX-r2-Bs-phe_5_signal31.573267
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1593.049561
RawQ2.353490
Spike_AFFX-r2-Bs-lys_5_signal22.944979
Signal(A)4.907619
%A39.508987
Signal(All)150.240204
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal285.116791
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.399784
Spike_AFFX-r2-Ec-bioD_avg-signal1280.180176
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.803158
Spike_AFFX-r2-Bs-lys_avg-signal24.649452
Spike_AFFX-r2-P1-cre_avg-signal5409.947266
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.687856
Spike_AFFX-r2-Bs-thr_3_signal117.220848
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal40.783817
Spike_AFFX-r2-Bs-dap_3_signal239.755905
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.646885
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.626953
#M385
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.735096
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.102425
Spike_AFFX-r2-Bs-thr_M_signal67.537575
Signal(P)251.658813
Spike_AFFX-r2-Bs-phe_3-5-ratio1.596280
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7125,Count:9
Spike_AFFX-r2-P1-cre_5_signal4773.327637
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9012
Signal(M)18.835625
BackgroundAvg:54.50,Std:0.31,Min:54.0,Max:55.4
Spike_AFFX-r2-Ec-bioC_avg-signal271.871887
Spike_AFFX-r2-Bs-dap_avg-signal188.569702
Spike_AFFX-r2-Bs-dap_3-5-ratio2.052719
Spike_AFFX-r2-Ec-bioB_5_signal70.929733
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.813983
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-6_1/13-g1-_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 ("Noir_568-6_1/13-g1-_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: Noir_568-6_1/13-g1-_Rep1_ATH1
Organism:
Alias: Col-gl1
Stock Code:
Age: 13 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium, long day conditions
Temperature22ºC
Tissue: Leaf
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.083668
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-ratio1.180324
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.171138
Spike_AFFX-r2-Bs-dap_5_signal140.124344
NoiseAvg:2.47,Std:0.06,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_signal62.277271
#P12184
Spike_AFFX-r2-Bs-phe_M_signal40.563633
Corner-Avg:7723,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal108.463943
Spike_AFFX-r2-Ec-bioB_3_signal87.639793
Spike_AFFX-r2-Bs-lys_M_signal16.149551
Spike_AFFX-r2-P1-cre_3_signal6128.761719
Spike_AFFX-r2-Bs-lys_3-5-ratio1.791049
Spike_AFFX-r2-Bs-dap_M_signal268.217285
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.464712
Spike_AFFX-r2-Ec-bioB_avg-signal90.312256
Spike_AFFX-r2-Bs-thr_avg-signal90.836983
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal885.746826
Spike_AFFX-r2-Bs-phe_5_signal43.490658
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1647.772339
RawQ2.542159
Spike_AFFX-r2-Bs-lys_5_signal19.362379
Signal(A)7.911519
%A44.340202
Signal(All)166.738953
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal403.458862
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal57.074635
Spike_AFFX-r2-Ec-bioD_avg-signal1266.759521
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P53.415169
Spike_AFFX-r2-Bs-lys_avg-signal23.396965
Spike_AFFX-r2-P1-cre_avg-signal5660.601563
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.244630
Spike_AFFX-r2-Bs-thr_3_signal91.218277
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-signal47.042973
Spike_AFFX-r2-Bs-dap_3_signal293.396301
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.860320
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal319.159637
#M512
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.678963
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.264129
Spike_AFFX-r2-Bs-thr_M_signal119.015396
Signal(P)304.448303
Spike_AFFX-r2-Bs-phe_3-5-ratio1.312342
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6386,Count:9
Spike_AFFX-r2-P1-cre_5_signal5192.441895
Spike_AFFX-r2-Bs-phe_M_detectionP
#A10114
Signal(M)27.148943
BackgroundAvg:57.31,Std:0.37,Min:56.5,Max:58.2
Spike_AFFX-r2-Ec-bioC_avg-signal361.309265
Spike_AFFX-r2-Bs-dap_avg-signal233.912643
Spike_AFFX-r2-Bs-dap_3-5-ratio2.093828
Spike_AFFX-r2-Ec-bioB_5_signal74.833023
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.083668
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-7_1/13-coi1+_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 ("Noir_568-7_1/13-coi1+_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: Noir_568-7_1/13-coi1+_Rep1_ATH1
Organism:
Alias: coi1-16
Stock Code:
Age: 13 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium + [50uM] MeJA, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.567429
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-ratio1.404721
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.289387
Spike_AFFX-r2-Bs-dap_5_signal183.531296
NoiseAvg:2.86,Std:0.08,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal56.435463
#P13592
Spike_AFFX-r2-Bs-phe_M_signal53.533203
Corner-Avg:17989,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal110.965820
Spike_AFFX-r2-Ec-bioB_3_signal95.780136
Spike_AFFX-r2-Bs-lys_M_signal21.186853
Spike_AFFX-r2-P1-cre_3_signal5957.963867
Spike_AFFX-r2-Bs-lys_3-5-ratio1.892076
Spike_AFFX-r2-Bs-dap_M_signal338.051483
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.221801
Spike_AFFX-r2-Ec-bioB_avg-signal93.676483
Spike_AFFX-r2-Bs-thr_avg-signal89.439606
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal927.175659
Spike_AFFX-r2-Bs-phe_5_signal75.463776
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1698.509888
RawQ2.559626
Spike_AFFX-r2-Bs-lys_5_signal27.198330
Signal(A)4.665083
%A38.526962
Signal(All)154.313049
Corner+Avg:270,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal247.302872
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal77.124352
Spike_AFFX-r2-Ec-bioD_avg-signal1312.842773
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.587898
Spike_AFFX-r2-Bs-lys_avg-signal33.282166
Spike_AFFX-r2-P1-cre_avg-signal5099.674316
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal125.388359
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal68.707115
Spike_AFFX-r2-Bs-dap_3_signal497.231567
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.831918
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal247.798370
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal51.461308
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.998000
Spike_AFFX-r2-Bs-thr_M_signal86.495010
Signal(P)255.378113
Spike_AFFX-r2-Bs-phe_3-5-ratio1.022005
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16541,Count:9
Spike_AFFX-r2-P1-cre_5_signal4241.384766
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8788
Signal(M)18.104031
BackgroundAvg:56.41,Std:0.56,Min:54.6,Max:57.5
Spike_AFFX-r2-Ec-bioC_avg-signal247.550629
Spike_AFFX-r2-Bs-dap_avg-signal339.604797
Spike_AFFX-r2-Bs-dap_3-5-ratio2.709247
Spike_AFFX-r2-Ec-bioB_5_signal74.283493
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.567429
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-8_1/13-coi1-_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 ("Noir_568-8_1/13-coi1-_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: Noir_568-8_1/13-coi1-_Rep1_ATH1
Organism:
Alias: coi1-16
Stock Code:
Age: 13 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.740191
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-ratio1.410426
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.279674
Spike_AFFX-r2-Bs-dap_5_signal159.593781
NoiseAvg:2.32,Std:0.07,Min:2.0,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal64.113167
#P12984
Spike_AFFX-r2-Bs-phe_M_signal47.571804
Corner-Avg:9249,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal131.422562
Spike_AFFX-r2-Ec-bioB_3_signal100.353210
Spike_AFFX-r2-Bs-lys_M_signal22.368521
Spike_AFFX-r2-P1-cre_3_signal8184.884766
Spike_AFFX-r2-Bs-lys_3-5-ratio2.065280
Spike_AFFX-r2-Bs-dap_M_signal316.812225
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.109061
Spike_AFFX-r2-Ec-bioB_avg-signal103.398888
Spike_AFFX-r2-Bs-thr_avg-signal98.447571
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1219.339355
Spike_AFFX-r2-Bs-phe_5_signal59.809204
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1825.283325
RawQ2.184544
Spike_AFFX-r2-Bs-lys_5_signal29.004673
Signal(A)5.091469
%A41.091625
Signal(All)166.135010
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal403.755371
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal69.233940
Spike_AFFX-r2-Ec-bioD_avg-signal1522.311279
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.922401
Spike_AFFX-r2-Bs-lys_avg-signal37.091984
Spike_AFFX-r2-P1-cre_avg-signal6994.006836
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.985971
Spike_AFFX-r2-Bs-thr_3_signal135.218597
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-signal58.871647
Spike_AFFX-r2-Bs-dap_3_signal408.208099
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.496944
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal396.953247
#M453
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal59.902760
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.017136
Spike_AFFX-r2-Bs-thr_M_signal96.010963
Signal(P)287.495178
Spike_AFFX-r2-Bs-phe_3-5-ratio1.157580
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6943,Count:9
Spike_AFFX-r2-P1-cre_5_signal5803.129395
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9373
Signal(M)19.823124
BackgroundAvg:51.29,Std:0.22,Min:50.5,Max:52.2
Spike_AFFX-r2-Ec-bioC_avg-signal400.354309
Spike_AFFX-r2-Bs-dap_avg-signal294.871368
Spike_AFFX-r2-Bs-dap_3-5-ratio2.557795
Spike_AFFX-r2-Ec-bioB_5_signal78.420891
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.740191
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-9_1/13-aos+_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 ("Noir_568-9_1/13-aos+_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: Noir_568-9_1/13-aos+_Rep1_ATH1
Organism:
Alias: aos
Stock Code:
Age: 13 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium + [50uM] MeJA, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.759831
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-ratio1.207831
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.132797
Spike_AFFX-r2-Bs-dap_5_signal144.854446
NoiseAvg:2.41,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_signal50.703251
#P13561
Spike_AFFX-r2-Bs-phe_M_signal31.944374
Corner-Avg:8978,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal130.338364
Spike_AFFX-r2-Ec-bioB_3_signal77.702408
Spike_AFFX-r2-Bs-lys_M_signal26.960079
Spike_AFFX-r2-P1-cre_3_signal5812.165527
Spike_AFFX-r2-Bs-lys_3-5-ratio2.236142
Spike_AFFX-r2-Bs-dap_M_signal251.763214
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.218975
Spike_AFFX-r2-Ec-bioB_avg-signal92.211395
Spike_AFFX-r2-Bs-thr_avg-signal99.023277
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal903.595032
Spike_AFFX-r2-Bs-phe_5_signal48.443443
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1528.322388
RawQ2.348088
Spike_AFFX-r2-Bs-lys_5_signal25.413597
Signal(A)4.675497
%A38.842613
Signal(All)147.724869
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal320.242523
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal53.550568
Spike_AFFX-r2-Ec-bioD_avg-signal1215.958740
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.451996
Spike_AFFX-r2-Bs-lys_avg-signal36.400692
Spike_AFFX-r2-P1-cre_avg-signal5312.116211
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal163.212479
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-signal44.646130
Spike_AFFX-r2-Bs-dap_3_signal328.973358
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.691380
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal290.460419
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.828407
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.102534
Spike_AFFX-r2-Bs-thr_M_signal83.154083
Signal(P)244.940231
Spike_AFFX-r2-Bs-phe_3-5-ratio1.105425
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5513,Count:9
Spike_AFFX-r2-P1-cre_5_signal4812.066895
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8860
Signal(M)16.824808
BackgroundAvg:53.89,Std:0.48,Min:52.7,Max:55.3
Spike_AFFX-r2-Ec-bioC_avg-signal305.351471
Spike_AFFX-r2-Bs-dap_avg-signal241.863663
Spike_AFFX-r2-Bs-dap_3-5-ratio2.271061
Spike_AFFX-r2-Ec-bioB_5_signal68.593414
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.759831
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-10_1/13-aos-_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 ("Noir_568-10_1/13-aos-_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: Noir_568-10_1/13-aos-_Rep1_ATH1
Organism:
Alias: aos
Stock Code:
Age: 13 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.673172
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-ratio1.320447
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.183491
Spike_AFFX-r2-Bs-dap_5_signal103.226479
NoiseAvg:2.53,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_signal53.491554
#P13042
Spike_AFFX-r2-Bs-phe_M_signal41.184162
Corner-Avg:8523,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.332596
Spike_AFFX-r2-Ec-bioB_3_signal75.197372
Spike_AFFX-r2-Bs-lys_M_signal13.689443
Spike_AFFX-r2-P1-cre_3_signal5917.409668
Spike_AFFX-r2-Bs-lys_3-5-ratio2.294423
Spike_AFFX-r2-Bs-dap_M_signal245.660477
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.555163
Spike_AFFX-r2-Ec-bioB_avg-signal76.689537
Spike_AFFX-r2-Bs-thr_avg-signal93.501366
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal975.095825
Spike_AFFX-r2-Bs-phe_5_signal35.965225
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1471.068237
RawQ2.457906
Spike_AFFX-r2-Bs-lys_5_signal20.078934
Signal(A)4.935067
%A40.968872
Signal(All)160.726120
Corner+Avg:134,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal306.145264
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.420727
Spike_AFFX-r2-Ec-bioD_avg-signal1223.082031
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.176678
Spike_AFFX-r2-Bs-lys_avg-signal26.612648
Spike_AFFX-r2-P1-cre_avg-signal5199.388672
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.854450
Spike_AFFX-r2-Bs-thr_3_signal136.679626
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-signal42.523373
Spike_AFFX-r2-Bs-dap_3_signal329.254150
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.508640
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal287.107452
#M423
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.069569
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.066309
Spike_AFFX-r2-Bs-thr_M_signal90.332909
Signal(P)276.930695
Spike_AFFX-r2-Bs-phe_3-5-ratio1.401930
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5695,Count:9
Spike_AFFX-r2-P1-cre_5_signal4481.367188
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9345
Signal(M)19.655560
BackgroundAvg:56.49,Std:0.29,Min:55.8,Max:57.4
Spike_AFFX-r2-Ec-bioC_avg-signal296.626343
Spike_AFFX-r2-Bs-dap_avg-signal226.047043
Spike_AFFX-r2-Bs-dap_3-5-ratio3.189629
Spike_AFFX-r2-Ec-bioB_5_signal63.538635
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.673172
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-11_1/19-gl+_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 ("Noir_568-11_1/19-gl+_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: Noir_568-11_1/19-gl+_Rep1_ATH1
Organism:
Alias: Col-gl1
Stock Code:
Age: 19 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium + [50uM] MeJA, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.558874
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-ratio1.142298
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.066914
Spike_AFFX-r2-Bs-dap_5_signal127.369904
NoiseAvg:2.68,Std:0.06,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_signal46.433434
#P13582
Spike_AFFX-r2-Bs-phe_M_signal33.978844
Corner-Avg:9006,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal116.627289
Spike_AFFX-r2-Ec-bioB_3_signal79.498337
Spike_AFFX-r2-Bs-lys_M_signal27.187496
Spike_AFFX-r2-P1-cre_3_signal5509.283203
Spike_AFFX-r2-Bs-lys_3-5-ratio2.185069
Spike_AFFX-r2-Bs-dap_M_signal256.508575
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.457988
Spike_AFFX-r2-Ec-bioB_avg-signal90.212685
Spike_AFFX-r2-Bs-thr_avg-signal98.326813
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal827.068176
Spike_AFFX-r2-Bs-phe_5_signal56.183647
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1355.320435
RawQ2.568116
Spike_AFFX-r2-Bs-lys_5_signal26.253004
Signal(A)3.515185
%A38.868916
Signal(All)147.202682
Corner+Avg:137,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal358.408386
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.492302
Spike_AFFX-r2-Ec-bioD_avg-signal1091.194336
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.544060
Spike_AFFX-r2-Bs-lys_avg-signal36.935043
Spike_AFFX-r2-P1-cre_avg-signal5166.132324
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.587023
Spike_AFFX-r2-Bs-thr_3_signal160.566238
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-signal42.218266
Spike_AFFX-r2-Bs-dap_3_signal357.467163
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.638705
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal287.210083
#M362
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.364628
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.247896
Spike_AFFX-r2-Bs-thr_M_signal87.980766
Signal(P)244.540741
Spike_AFFX-r2-Bs-phe_3-5-ratio0.649518
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6549,Count:9
Spike_AFFX-r2-P1-cre_5_signal4822.981445
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8866
Signal(M)14.296221
BackgroundAvg:62.36,Std:0.40,Min:60.9,Max:63.8
Spike_AFFX-r2-Ec-bioC_avg-signal322.809235
Spike_AFFX-r2-Bs-dap_avg-signal247.115189
Spike_AFFX-r2-Bs-dap_3-5-ratio2.806528
Spike_AFFX-r2-Ec-bioB_5_signal74.512436
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.558874
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-12_1/19-gl-_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 ("Noir_568-12_1/19-gl-_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: Noir_568-12_1/19-gl-_Rep1_ATH1
Organism:
Alias: Col-gl1
Stock Code:
Age: 19 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.672416
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-ratio1.399270
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.064481
Spike_AFFX-r2-Bs-dap_5_signal124.361465
NoiseAvg:2.67,Std:0.08,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_signal50.441383
#P13071
Spike_AFFX-r2-Bs-phe_M_signal45.799801
Corner-Avg:9188,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal101.915062
Spike_AFFX-r2-Ec-bioB_3_signal86.750244
Spike_AFFX-r2-Bs-lys_M_signal14.127426
Spike_AFFX-r2-P1-cre_3_signal6662.933594
Spike_AFFX-r2-Bs-lys_3-5-ratio1.471018
Spike_AFFX-r2-Bs-dap_M_signal215.356781
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.855369
Spike_AFFX-r2-Ec-bioB_avg-signal90.053551
Spike_AFFX-r2-Bs-thr_avg-signal78.454887
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal951.099792
Spike_AFFX-r2-Bs-phe_5_signal49.153542
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1572.258911
RawQ2.600241
Spike_AFFX-r2-Bs-lys_5_signal29.569164
Signal(A)4.540431
%A41.122314
Signal(All)158.959991
Corner+Avg:138,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal350.018311
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal38.278778
Spike_AFFX-r2-Ec-bioD_avg-signal1261.679321
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.303814
Spike_AFFX-r2-Bs-lys_avg-signal29.064451
Spike_AFFX-r2-P1-cre_avg-signal5712.327148
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.573871
Spike_AFFX-r2-Bs-thr_3_signal93.587372
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-signal44.410706
Spike_AFFX-r2-Bs-dap_3_signal351.115814
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.653096
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal339.752167
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.496761
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.030217
Spike_AFFX-r2-Bs-thr_M_signal91.335892
Signal(P)273.665436
Spike_AFFX-r2-Bs-phe_3-5-ratio0.778759
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6768,Count:9
Spike_AFFX-r2-P1-cre_5_signal4761.720703
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9380
Signal(M)17.290092
BackgroundAvg:61.75,Std:0.77,Min:60.3,Max:63.7
Spike_AFFX-r2-Ec-bioC_avg-signal344.885254
Spike_AFFX-r2-Bs-dap_avg-signal230.278015
Spike_AFFX-r2-Bs-dap_3-5-ratio2.823349
Spike_AFFX-r2-Ec-bioB_5_signal81.495331
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.672416
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-13_1/19-coi1+_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 ("Noir_568-13_1/19-coi1+_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: Noir_568-13_1/19-coi1+_Rep1_ATH1
Organism:
Alias: coi1-16
Stock Code:
Age: 19 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium + [50uM] MeJA, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.554408
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-ratio1.254631
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.962035
Spike_AFFX-r2-Bs-dap_5_signal33.125118
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_signal21.958445
#P13081
Spike_AFFX-r2-Bs-phe_M_signal32.803165
Corner-Avg:10932,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.958344
Spike_AFFX-r2-Ec-bioB_3_signal80.544731
Spike_AFFX-r2-Bs-lys_M_signal9.079127
Spike_AFFX-r2-P1-cre_3_signal5472.838379
Spike_AFFX-r2-Bs-lys_3-5-ratio3.496578
Spike_AFFX-r2-Bs-dap_M_signal143.025589
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.340302
Spike_AFFX-r2-Ec-bioB_avg-signal88.075462
Spike_AFFX-r2-Bs-thr_avg-signal46.698761
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal814.829163
Spike_AFFX-r2-Bs-phe_5_signal29.043617
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1533.362549
RawQ2.820547
Spike_AFFX-r2-Bs-lys_5_signal16.633930
Signal(A)4.429941
%A40.859272
Signal(All)155.676590
Corner+Avg:182,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal332.501526
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.226055
Spike_AFFX-r2-Ec-bioD_avg-signal1174.095825
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.347656
Spike_AFFX-r2-Bs-lys_avg-signal27.958298
Spike_AFFX-r2-P1-cre_avg-signal4917.474609
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.793073
Spike_AFFX-r2-Bs-thr_3_signal73.347832
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-signal32.690945
Spike_AFFX-r2-Bs-dap_3_signal259.083588
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.881821
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal324.078888
#M409
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal58.161831
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.025989
Spike_AFFX-r2-Bs-thr_M_signal44.790005
Signal(P)267.707672
Spike_AFFX-r2-Bs-phe_3-5-ratio1.247298
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7370,Count:9
Spike_AFFX-r2-P1-cre_5_signal4362.110352
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9320
Signal(M)19.099651
BackgroundAvg:66.62,Std:1.29,Min:62.5,Max:69.3
Spike_AFFX-r2-Ec-bioC_avg-signal328.290222
Spike_AFFX-r2-Bs-dap_avg-signal145.078110
Spike_AFFX-r2-Bs-dap_3-5-ratio7.821363
Spike_AFFX-r2-Ec-bioB_5_signal83.723282
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.554408
NF1.000000
HZ4
Tau0.015000

Slide: Noir_568-14_1/19-coi1-_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 ("Noir_568-14_1/19-coi1-_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: Noir_568-14_1/19-coi1-_Rep1_ATH1
Organism:
Alias: coi1-16
Stock Code:
Age: 19 days
Growth Conditions:
in vitro cultureContinuous growth on MS medium, long day conditions
Temperature22ºC
Tissue: Leaf
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:0.641812
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-ratio1.185896
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.142645
Spike_AFFX-r2-Bs-dap_5_signal14.819910
NoiseAvg:2.91,Std:0.11,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.263088
#P13048
Spike_AFFX-r2-Bs-phe_M_signal33.410080
Corner-Avg:12705,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal112.729172
Spike_AFFX-r2-Ec-bioB_3_signal103.227859
Spike_AFFX-r2-Bs-lys_M_signal19.970221
Spike_AFFX-r2-P1-cre_3_signal5619.158691
Spike_AFFX-r2-Bs-lys_3-5-ratio1.854473
Spike_AFFX-r2-Bs-dap_M_signal122.123207
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.375877
Spike_AFFX-r2-Ec-bioB_avg-signal102.099388
Spike_AFFX-r2-Bs-thr_avg-signal40.316238
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal898.557556
Spike_AFFX-r2-Bs-phe_5_signal25.131142
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1754.809204
RawQ2.764350
Spike_AFFX-r2-Bs-lys_5_signal27.089010
Signal(A)4.820230
%A40.854889
Signal(All)155.509644
Corner+Avg:196,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal371.814362
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.633354
Spike_AFFX-r2-Ec-bioD_avg-signal1326.683350
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.202980
Spike_AFFX-r2-Bs-lys_avg-signal32.431690
Spike_AFFX-r2-P1-cre_avg-signal5178.741211
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.942131
Spike_AFFX-r2-Bs-thr_3_signal71.300735
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-signal37.058193
Spike_AFFX-r2-Bs-dap_3_signal305.760223
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.952918
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal357.725189
#M443
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.235844
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.039385
Spike_AFFX-r2-Bs-thr_M_signal36.384884
Signal(P)267.777863
Spike_AFFX-r2-Bs-phe_3-5-ratio2.094348
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9783,Count:9
Spike_AFFX-r2-P1-cre_5_signal4738.323730
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9319
Signal(M)18.712378
BackgroundAvg:64.99,Std:1.64,Min:60.4,Max:68.2
Spike_AFFX-r2-Ec-bioC_avg-signal364.769775
Spike_AFFX-r2-Bs-dap_avg-signal147.567780
Spike_AFFX-r2-Bs-dap_3-5-ratio20.631720
Spike_AFFX-r2-Ec-bioB_5_signal90.341125
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.641812
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team