NASC's International Affymetrix Service

AI logo

NASCArrays

home, selection, spot history, gene swinger, two gene scatterplot, digital northern, bulk gene download, tutorial, help, Affymetrix site, NASC

Experiment: Jasmonate Continuous Growth Control

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-574

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 stratificationTreatment: 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:10
 
Experimental Parameters:
parameterdevelopmental_stage
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Noir: Jasmonate Continuous Growth Control

Slide: Noir_574-1_2-9_gl1+_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_574-1_2-9_gl1+_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_574-1_2-9_gl1+_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:0.567962
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.935394
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.113382
Spike_AFFX-r2-Bs-dap_5_signal86.950348
NoiseAvg:2.41,Std:0.09,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.740465
#P14290
Spike_AFFX-r2-Bs-phe_M_signal33.494637
Corner-Avg:10370,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.299927
Spike_AFFX-r2-Ec-bioB_3_signal56.946438
Spike_AFFX-r2-Bs-lys_M_signal12.111294
Spike_AFFX-r2-P1-cre_3_signal2890.407471
Spike_AFFX-r2-Bs-lys_3-5-ratio2.035580
Spike_AFFX-r2-Bs-dap_M_signal259.621460
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.941637
Spike_AFFX-r2-Ec-bioB_avg-signal61.131207
Spike_AFFX-r2-Bs-thr_avg-signal107.251152
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal412.852325
Spike_AFFX-r2-Bs-phe_5_signal40.516151
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal777.686401
RawQ2.481674
Spike_AFFX-r2-Bs-lys_5_signal27.615223
Signal(A)3.123895
%A35.909687
Signal(All)146.667419
Corner+Avg:151,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal215.514008
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.430367
Spike_AFFX-r2-Ec-bioD_avg-signal595.269348
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.647961
Spike_AFFX-r2-Bs-lys_avg-signal31.979843
Spike_AFFX-r2-P1-cre_avg-signal2990.225830
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.442350
Spike_AFFX-r2-Bs-thr_3_signal170.765411
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal45.480389
Spike_AFFX-r2-Bs-dap_3_signal282.200104
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.883691
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal225.023483
#M329
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.213009
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.957740
Spike_AFFX-r2-Bs-thr_M_signal122.247551
Signal(P)232.006790
Spike_AFFX-r2-Bs-phe_3-5-ratio1.540876
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9015,Count:9
Spike_AFFX-r2-P1-cre_5_signal3090.044189
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8191
Signal(M)13.735186
BackgroundAvg:55.06,Std:0.55,Min:53.6,Max:56.3
Spike_AFFX-r2-Ec-bioC_avg-signal220.268738
Spike_AFFX-r2-Bs-dap_avg-signal209.590622
Spike_AFFX-r2-Bs-dap_3-5-ratio3.245532
Spike_AFFX-r2-Ec-bioB_5_signal51.147243
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.567962
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-2_2-9_gl1-_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_574-2_2-9_gl1-_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_574-2_2-9_gl1-_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:0.566601
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-ratio1.323398
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.536589
Spike_AFFX-r2-Bs-dap_5_signal37.452068
NoiseAvg:2.72,Std:0.07,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.571056
#P13892
Spike_AFFX-r2-Bs-phe_M_signal39.210079
Corner-Avg:13384,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal94.035912
Spike_AFFX-r2-Ec-bioB_3_signal88.215408
Spike_AFFX-r2-Bs-lys_M_signal9.796694
Spike_AFFX-r2-P1-cre_3_signal4394.524414
Spike_AFFX-r2-Bs-lys_3-5-ratio1.889393
Spike_AFFX-r2-Bs-dap_M_signal196.955444
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.570015
Spike_AFFX-r2-Ec-bioB_avg-signal79.887062
Spike_AFFX-r2-Bs-thr_avg-signal74.380989
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal696.320984
Spike_AFFX-r2-Bs-phe_5_signal33.587093
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1409.038452
RawQ2.610727
Spike_AFFX-r2-Bs-lys_5_signal25.448057
Signal(A)3.706407
%A37.562473
Signal(All)153.098557
Corner+Avg:205,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.058472
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.216122
Spike_AFFX-r2-Ec-bioD_avg-signal1052.679688
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.903114
Spike_AFFX-r2-Bs-lys_avg-signal27.775377
Spike_AFFX-r2-P1-cre_avg-signal3857.580566
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.534415
Spike_AFFX-r2-Bs-thr_3_signal112.709160
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-signal35.671097
Spike_AFFX-r2-Bs-dap_3_signal213.132889
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.023547
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal281.109650
#M350
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.081383
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.811279
Spike_AFFX-r2-Bs-thr_M_signal78.862755
Signal(P)248.721924
Spike_AFFX-r2-Bs-phe_3-5-ratio1.018728
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10676,Count:9
Spike_AFFX-r2-P1-cre_5_signal3320.636475
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8568
Signal(M)14.790217
BackgroundAvg:63.29,Std:0.18,Min:62.7,Max:63.7
Spike_AFFX-r2-Ec-bioC_avg-signal254.584061
Spike_AFFX-r2-Bs-dap_avg-signal149.180130
Spike_AFFX-r2-Bs-dap_3-5-ratio5.690817
Spike_AFFX-r2-Ec-bioB_5_signal57.409885
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.566601
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-3_2-9_coi1-16 +_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_574-3_2-9_coi1-16 +_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_574-3_2-9_coi1-16 +_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:0.598326
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-ratio1.283959
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.124496
Spike_AFFX-r2-Bs-dap_5_signal73.673149
NoiseAvg:2.47,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_signal30.821218
#P13961
Spike_AFFX-r2-Bs-phe_M_signal51.697617
Corner-Avg:12041,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.009743
Spike_AFFX-r2-Ec-bioB_3_signal71.385376
Spike_AFFX-r2-Bs-lys_M_signal15.683554
Spike_AFFX-r2-P1-cre_3_signal4296.001465
Spike_AFFX-r2-Bs-lys_3-5-ratio2.156161
Spike_AFFX-r2-Bs-dap_M_signal256.612610
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.139445
Spike_AFFX-r2-Ec-bioB_avg-signal74.625740
Spike_AFFX-r2-Bs-thr_avg-signal87.143730
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal638.370605
Spike_AFFX-r2-Bs-phe_5_signal53.755867
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1299.610962
RawQ2.427034
Spike_AFFX-r2-Bs-lys_5_signal29.500662
Signal(A)3.781521
%A37.246822
Signal(All)151.267319
Corner+Avg:189,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal273.788635
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.557678
Spike_AFFX-r2-Ec-bioD_avg-signal968.990784
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.205612
Spike_AFFX-r2-Bs-lys_avg-signal36.264126
Spike_AFFX-r2-P1-cre_avg-signal3820.951416
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.547567
Spike_AFFX-r2-Bs-thr_3_signal127.582748
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-signal50.003723
Spike_AFFX-r2-Bs-dap_3_signal343.990601
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.035825
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal297.987549
#M353
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal63.608166
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.918792
Spike_AFFX-r2-Bs-thr_M_signal103.027214
Signal(P)244.443329
Spike_AFFX-r2-Bs-phe_3-5-ratio0.828890
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9137,Count:9
Spike_AFFX-r2-P1-cre_5_signal3345.901367
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8496
Signal(M)15.882861
BackgroundAvg:54.96,Std:0.39,Min:54.1,Max:56.3
Spike_AFFX-r2-Ec-bioC_avg-signal285.888092
Spike_AFFX-r2-Bs-dap_avg-signal224.758789
Spike_AFFX-r2-Bs-dap_3-5-ratio4.669145
Spike_AFFX-r2-Ec-bioB_5_signal63.482105
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.598326
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-4_2-9_coi1-16 -_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_574-4_2-9_coi1-16 -_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_574-4_2-9_coi1-16 -_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:0.602055
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.906871
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.273109
Spike_AFFX-r2-Bs-dap_5_signal94.861031
NoiseAvg:2.56,Std:0.11,Min:2.3,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_signal33.001434
#P13713
Spike_AFFX-r2-Bs-phe_M_signal40.019367
Corner-Avg:11914,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.996468
Spike_AFFX-r2-Ec-bioB_3_signal69.023773
Spike_AFFX-r2-Bs-lys_M_signal16.048946
Spike_AFFX-r2-P1-cre_3_signal3158.248047
Spike_AFFX-r2-Bs-lys_3-5-ratio1.916392
Spike_AFFX-r2-Bs-dap_M_signal234.565704
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.186671
Spike_AFFX-r2-Ec-bioB_avg-signal69.745644
Spike_AFFX-r2-Bs-thr_avg-signal83.972954
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal590.844543
Spike_AFFX-r2-Bs-phe_5_signal60.743179
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1085.380127
RawQ2.402030
Spike_AFFX-r2-Bs-lys_5_signal29.995205
Signal(A)4.224347
%A38.158703
Signal(All)153.146866
Corner+Avg:187,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal264.644867
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal68.137993
Spike_AFFX-r2-Ec-bioD_avg-signal838.112305
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.118370
Spike_AFFX-r2-Bs-lys_avg-signal34.508911
Spike_AFFX-r2-P1-cre_avg-signal3320.413086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal105.164734
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-signal56.300182
Spike_AFFX-r2-Bs-dap_3_signal346.916443
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.836998
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal281.104797
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.482582
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.941446
Spike_AFFX-r2-Bs-thr_M_signal113.752701
Signal(P)251.568527
Spike_AFFX-r2-Bs-phe_3-5-ratio1.121739
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9843,Count:9
Spike_AFFX-r2-P1-cre_5_signal3482.578125
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8704
Signal(M)17.180998
BackgroundAvg:59.01,Std:0.73,Min:57.1,Max:60.6
Spike_AFFX-r2-Ec-bioC_avg-signal272.874817
Spike_AFFX-r2-Bs-dap_avg-signal225.447739
Spike_AFFX-r2-Bs-dap_3-5-ratio3.657102
Spike_AFFX-r2-Ec-bioB_5_signal54.216694
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.602055
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-5_2-13_gl1+_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_574-5_2-13_gl1+_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_574-5_2-13_gl1+_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:0.445709
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-ratio1.451766
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.258713
Spike_AFFX-r2-Bs-dap_5_signal93.844482
NoiseAvg:2.56,Std:0.12,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal42.767246
#P14267
Spike_AFFX-r2-Bs-phe_M_signal41.894909
Corner-Avg:12838,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.665901
Spike_AFFX-r2-Ec-bioB_3_signal63.525284
Spike_AFFX-r2-Bs-lys_M_signal21.260639
Spike_AFFX-r2-P1-cre_3_signal4556.005371
Spike_AFFX-r2-Bs-lys_3-5-ratio1.075683
Spike_AFFX-r2-Bs-dap_M_signal298.598022
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.155490
Spike_AFFX-r2-Ec-bioB_avg-signal66.553215
Spike_AFFX-r2-Bs-thr_avg-signal106.840752
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal577.240112
Spike_AFFX-r2-Bs-phe_5_signal62.549534
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1026.254272
RawQ2.374360
Spike_AFFX-r2-Bs-lys_5_signal37.208786
Signal(A)2.830562
%A35.861465
Signal(All)144.483551
Corner+Avg:203,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal263.975403
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal53.891155
Spike_AFFX-r2-Ec-bioD_avg-signal801.747192
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.547127
Spike_AFFX-r2-Bs-lys_avg-signal32.831432
Spike_AFFX-r2-P1-cre_avg-signal3847.128418
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal177.718887
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-signal52.778534
Spike_AFFX-r2-Bs-dap_3_signal379.748840
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.777864
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.824265
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.024876
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.217462
Spike_AFFX-r2-Bs-thr_M_signal100.036133
Signal(P)229.079880
Spike_AFFX-r2-Bs-phe_3-5-ratio0.861576
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9054,Count:9
Spike_AFFX-r2-P1-cre_5_signal3138.251465
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8180
Signal(M)11.661283
BackgroundAvg:52.97,Std:0.77,Min:51.6,Max:55.1
Spike_AFFX-r2-Ec-bioC_avg-signal240.399841
Spike_AFFX-r2-Bs-dap_avg-signal257.397125
Spike_AFFX-r2-Bs-dap_3-5-ratio4.046576
Spike_AFFX-r2-Ec-bioB_5_signal50.468445
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.445709
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-6_2-13_gl1-_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_574-6_2-13_gl1-_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_574-6_2-13_gl1-_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:0.504373
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-ratio1.420152
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.197139
Spike_AFFX-r2-Bs-dap_5_signal68.572067
NoiseAvg:2.99,Std:0.14,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_signal29.638075
#P14123
Spike_AFFX-r2-Bs-phe_M_signal49.140400
Corner-Avg:13840,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal78.279388
Spike_AFFX-r2-Ec-bioB_3_signal59.239113
Spike_AFFX-r2-Bs-lys_M_signal10.211535
Spike_AFFX-r2-P1-cre_3_signal4080.743408
Spike_AFFX-r2-Bs-lys_3-5-ratio2.890796
Spike_AFFX-r2-Bs-dap_M_signal198.557373
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.056000
Spike_AFFX-r2-Ec-bioB_avg-signal62.334137
Spike_AFFX-r2-Bs-thr_avg-signal76.312355
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal541.421387
Spike_AFFX-r2-Bs-phe_5_signal40.732609
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal975.953491
RawQ2.788620
Spike_AFFX-r2-Bs-lys_5_signal21.650740
Signal(A)3.213649
%A36.637440
Signal(All)148.867126
Corner+Avg:211,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal189.666321
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal57.292908
Spike_AFFX-r2-Ec-bioD_avg-signal758.687439
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.915825
Spike_AFFX-r2-Bs-lys_avg-signal31.483385
Spike_AFFX-r2-P1-cre_avg-signal3477.099609
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.446734
Spike_AFFX-r2-Bs-thr_3_signal120.212029
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal49.055302
Spike_AFFX-r2-Bs-dap_3_signal237.442368
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.802577
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal232.738922
#M330
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal62.587879
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.814932
Spike_AFFX-r2-Bs-thr_M_signal79.086952
Signal(P)238.210861
Spike_AFFX-r2-Bs-phe_3-5-ratio1.406561
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10863,Count:9
Spike_AFFX-r2-P1-cre_5_signal2873.455566
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8357
Signal(M)13.790168
BackgroundAvg:74.11,Std:1.91,Min:66.9,Max:77.6
Spike_AFFX-r2-Ec-bioC_avg-signal211.202621
Spike_AFFX-r2-Bs-dap_avg-signal168.190613
Spike_AFFX-r2-Bs-dap_3-5-ratio3.462669
Spike_AFFX-r2-Ec-bioB_5_signal49.483921
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.504373
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-7_2-13_coi1-16 +_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_574-7_2-13_coi1-16 +_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_574-7_2-13_coi1-16 +_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:0.626804
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-ratio1.166022
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.201061
Spike_AFFX-r2-Bs-dap_5_signal108.145340
NoiseAvg:2.68,Std:0.08,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_signal57.632801
#P13768
Spike_AFFX-r2-Bs-phe_M_signal53.101315
Corner-Avg:10328,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.706787
Spike_AFFX-r2-Ec-bioB_3_signal64.855873
Spike_AFFX-r2-Bs-lys_M_signal16.098654
Spike_AFFX-r2-P1-cre_3_signal3893.748779
Spike_AFFX-r2-Bs-lys_3-5-ratio0.950832
Spike_AFFX-r2-Bs-dap_M_signal311.481628
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.833624
Spike_AFFX-r2-Ec-bioB_avg-signal68.520485
Spike_AFFX-r2-Bs-thr_avg-signal118.883942
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal646.146912
Spike_AFFX-r2-Bs-phe_5_signal65.301903
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1036.271729
RawQ2.732038
Spike_AFFX-r2-Bs-lys_5_signal46.005333
Signal(A)3.716952
%A37.978958
Signal(All)148.576645
Corner+Avg:169,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal265.412231
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal69.308807
Spike_AFFX-r2-Ec-bioD_avg-signal841.209351
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.359493
Spike_AFFX-r2-Bs-lys_avg-signal35.282444
Spike_AFFX-r2-P1-cre_avg-signal3616.546875
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.661552
Spike_AFFX-r2-Bs-thr_3_signal163.309677
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-signal62.570679
Spike_AFFX-r2-Bs-dap_3_signal343.086273
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.603771
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal276.191864
#M379
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.743340
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.960971
Spike_AFFX-r2-Bs-thr_M_signal135.709335
Signal(P)243.408829
Spike_AFFX-r2-Bs-phe_3-5-ratio1.061360
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7534,Count:9
Spike_AFFX-r2-P1-cre_5_signal3339.344727
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8663
Signal(M)14.724730
BackgroundAvg:64.23,Std:0.72,Min:62.5,Max:66.1
Spike_AFFX-r2-Ec-bioC_avg-signal270.802063
Spike_AFFX-r2-Bs-dap_avg-signal254.237732
Spike_AFFX-r2-Bs-dap_3-5-ratio3.172456
Spike_AFFX-r2-Ec-bioB_5_signal53.998806
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.626804
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-8_2-13_coi1-16 -_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_574-8_2-13_coi1-16 -_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_574-8_2-13_coi1-16 -_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:0.426849
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-ratio1.289915
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.494846
Spike_AFFX-r2-Bs-dap_5_signal80.262833
NoiseAvg:3.06,Std:0.07,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_signal40.822849
#P13740
Spike_AFFX-r2-Bs-phe_M_signal43.914993
Corner-Avg:11758,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal62.059280
Spike_AFFX-r2-Ec-bioB_3_signal55.023968
Spike_AFFX-r2-Bs-lys_M_signal16.293324
Spike_AFFX-r2-P1-cre_3_signal3659.430176
Spike_AFFX-r2-Bs-lys_3-5-ratio2.171390
Spike_AFFX-r2-Bs-dap_M_signal274.659698
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.415281
Spike_AFFX-r2-Ec-bioB_avg-signal51.297455
Spike_AFFX-r2-Bs-thr_avg-signal93.278412
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal515.850098
Spike_AFFX-r2-Bs-phe_5_signal57.670551
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal961.618591
RawQ2.927528
Spike_AFFX-r2-Bs-lys_5_signal32.436539
Signal(A)3.063288
%A38.237614
Signal(All)149.054337
Corner+Avg:182,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal202.983734
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal60.519882
Spike_AFFX-r2-Ec-bioD_avg-signal738.734375
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.236740
Spike_AFFX-r2-Bs-lys_avg-signal39.720749
Spike_AFFX-r2-P1-cre_avg-signal3248.192383
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.525647
Spike_AFFX-r2-Bs-thr_3_signal139.421494
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-signal54.035141
Spike_AFFX-r2-Bs-dap_3_signal314.312073
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.864143
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal250.365463
#M348
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal70.432381
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.810750
Spike_AFFX-r2-Bs-thr_M_signal99.590897
Signal(P)245.183914
Spike_AFFX-r2-Bs-phe_3-5-ratio1.049407
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8927,Count:9
Spike_AFFX-r2-P1-cre_5_signal2836.954346
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8722
Signal(M)12.598532
BackgroundAvg:71.79,Std:0.97,Min:69.1,Max:74.1
Spike_AFFX-r2-Ec-bioC_avg-signal226.674591
Spike_AFFX-r2-Bs-dap_avg-signal223.078201
Spike_AFFX-r2-Bs-dap_3-5-ratio3.916035
Spike_AFFX-r2-Ec-bioB_5_signal36.809113
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.426849
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-9_2-13_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_574-9_2-13_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_574-9_2-13_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:0.669869
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-ratio1.030487
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.188754
Spike_AFFX-r2-Bs-dap_5_signal105.975052
NoiseAvg:2.35,Std:0.13,Min:2.0,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal45.994171
#P13556
Spike_AFFX-r2-Bs-phe_M_signal52.410023
Corner-Avg:11570,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.570015
Spike_AFFX-r2-Ec-bioB_3_signal63.970406
Spike_AFFX-r2-Bs-lys_M_signal31.247501
Spike_AFFX-r2-P1-cre_3_signal3590.509033
Spike_AFFX-r2-Bs-lys_3-5-ratio1.917475
Spike_AFFX-r2-Bs-dap_M_signal363.469757
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.519536
Spike_AFFX-r2-Ec-bioB_avg-signal71.451141
Spike_AFFX-r2-Bs-thr_avg-signal166.755463
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal611.771118
Spike_AFFX-r2-Bs-phe_5_signal79.727074
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1153.763184
RawQ2.396760
Spike_AFFX-r2-Bs-lys_5_signal38.494884
Signal(A)3.444998
%A38.890839
Signal(All)149.736877
Corner+Avg:172,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal260.954834
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal84.306389
Spike_AFFX-r2-Ec-bioD_avg-signal882.767151
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.430073
Spike_AFFX-r2-Bs-lys_avg-signal47.851791
Spike_AFFX-r2-P1-cre_avg-signal3537.396240
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.679088
Spike_AFFX-r2-Bs-thr_3_signal299.860626
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-signal72.147827
Spike_AFFX-r2-Bs-dap_3_signal497.979218
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.885939
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal217.171707
#M383
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal73.812988
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.201606
Spike_AFFX-r2-Bs-thr_M_signal154.411606
Signal(P)249.299805
Spike_AFFX-r2-Bs-phe_3-5-ratio1.057437
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8327,Count:9
Spike_AFFX-r2-P1-cre_5_signal3484.283447
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8871
Signal(M)14.175725
BackgroundAvg:57.84,Std:0.76,Min:56.0,Max:59.7
Spike_AFFX-r2-Ec-bioC_avg-signal239.063263
Spike_AFFX-r2-Bs-dap_avg-signal322.474670
Spike_AFFX-r2-Bs-dap_3-5-ratio4.699023
Spike_AFFX-r2-Ec-bioB_5_signal53.813004
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.669869
NF1.000000
HZ4
Tau0.015000

Slide: Noir_574-10_2-13_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_574-10_2-13_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_574-10_2-13_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:0.655249
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-ratio1.613951
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.217609
Spike_AFFX-r2-Bs-dap_5_signal101.791687
NoiseAvg:2.63,Std:0.05,Min:2.5,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_signal46.616760
#P13316
Spike_AFFX-r2-Bs-phe_M_signal40.425156
Corner-Avg:11603,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal110.597855
Spike_AFFX-r2-Ec-bioB_3_signal80.858162
Spike_AFFX-r2-Bs-lys_M_signal18.582523
Spike_AFFX-r2-P1-cre_3_signal6044.478516
Spike_AFFX-r2-Bs-lys_3-5-ratio1.154008
Spike_AFFX-r2-Bs-dap_M_signal288.874298
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.798102
Spike_AFFX-r2-Ec-bioB_avg-signal85.954445
Spike_AFFX-r2-Bs-thr_avg-signal86.154442
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal607.801880
Spike_AFFX-r2-Bs-phe_5_signal33.615280
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1264.422607
RawQ2.620764
Spike_AFFX-r2-Bs-lys_5_signal37.139580
Signal(A)4.231843
%A39.886013
Signal(All)155.291718
Corner+Avg:172,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal348.825653
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal43.460461
Spike_AFFX-r2-Ec-bioD_avg-signal936.112244
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.377903
Spike_AFFX-r2-Bs-lys_avg-signal32.860493
Spike_AFFX-r2-P1-cre_avg-signal4894.811523
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.736081
Spike_AFFX-r2-Bs-thr_3_signal130.438446
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-signal39.166965
Spike_AFFX-r2-Bs-dap_3_signal324.763428
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.080320
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal365.106964
#M396
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.859383
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.955407
Spike_AFFX-r2-Bs-thr_M_signal81.408104
Signal(P)262.609711
Spike_AFFX-r2-Bs-phe_3-5-ratio1.292878
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9383,Count:9
Spike_AFFX-r2-P1-cre_5_signal3745.144287
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9098
Signal(M)17.151545
BackgroundAvg:63.74,Std:0.53,Min:62.3,Max:65.1
Spike_AFFX-r2-Ec-bioC_avg-signal356.966309
Spike_AFFX-r2-Bs-dap_avg-signal238.476456
Spike_AFFX-r2-Bs-dap_3-5-ratio3.190471
Spike_AFFX-r2-Ec-bioB_5_signal66.407310
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.655249
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team