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Experiment: Using transcriptome analysis to compare gene expression of prt6 and Col-0 seed during germination and in response to Absisic Acid (ABA).

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-637

Absisic Acid (ABA) signaling for seed germination and seedling establishment is controlled by the N-end rule pathway of targeted proteolysis (Holman et al., 2009). In Arabidopsis thaliana, two components of this pathway, PROTEOLYSIS6 (PRT6) and arginyl-tRNA: protein arginyltransferase (ATE) have been shown to regulate seedling lipid breakdown and ABA sensitivity to germination (Holman et al., 2009).In these experiments, the transcriptome profile of after-ripened prt6 seed during germination on water agarose will be compared with Col-0 seed at the same stage. Also, the transcriptome profile of prt6 seed in response to ABA will be compared to that of WT seed. Seed will be imbibed on water agarose with an ABA concentration that will prevent germination- 1 µM for prt6 and 10 µM for Col-0. This will aid our understanding of the N-end rule pathway in regulating ABA signaling controlling germination and dormancy.Reference List1. Holman TJ, Jones PD, Russell L, Medhurst A, Ubeda-Thomas S, Talloji P, Marquez J, Schmuths H, Swee-Ang T, Taylor I, Footitt S, Bachmair A, Theodoulou FL, Holdsworth MJ (2009). The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. PNAS. 106:4549-4554.

About the Experimenter

Name:Miss Nurulhikma Md Isa
Head of Lab Name: Mike Holdsworth
Lab:
Address:Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham
Sutton Bonington Campus, College Road, Sutton Bonington, Nottinghamshire, LE12 5RD, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 0044 115 9516235
Fax Number: 0044 115 9516060

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; strain_or_line_design
Number of Slides:12
 
Experimental Parameters:
parameter compound_based_treatment
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Md Isa: Using transcriptome analysis to compare gene expression of prt6 and Col-0 seed during germination and in response to Absisic Acid (ABA).

Slide: Nurulhikma_637-1_prt6-1-on-water-agarose_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 ("Nurulhikma_637-1_prt6-1-on-water-agarose_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-1_prt6-1-on-water-agarose_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: prt6-1
Stock Code: N9873
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:0.993558
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-ratio1.048544
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.113961
Spike_AFFX-r2-Bs-dap_5_signal95.520554
NoiseAvg:2.31,Std:0.12,Min:2.1,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_signal30.819717
#P13299
Spike_AFFX-r2-Bs-phe_M_signal23.982880
Corner-Avg:11679,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal199.106491
Spike_AFFX-r2-Ec-bioB_3_signal154.005859
Spike_AFFX-r2-Bs-lys_M_signal24.689440
Spike_AFFX-r2-P1-cre_3_signal7466.318848
Spike_AFFX-r2-Bs-lys_3-5-ratio1.211336
Spike_AFFX-r2-Bs-dap_M_signal191.993515
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.476278
Spike_AFFX-r2-Ec-bioB_avg-signal163.787659
Spike_AFFX-r2-Bs-thr_avg-signal95.293396
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1586.574585
Spike_AFFX-r2-Bs-phe_5_signal25.480774
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2505.484131
RawQ2.329713
Spike_AFFX-r2-Bs-lys_5_signal26.177305
Signal(A)4.440340
%A40.179745
Signal(All)152.981689
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal531.876282
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal56.103622
Spike_AFFX-r2-Ec-bioD_avg-signal2046.029297
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.303375
Spike_AFFX-r2-Bs-lys_avg-signal27.525419
Spike_AFFX-r2-P1-cre_avg-signal7293.485352
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.516879
Spike_AFFX-r2-Bs-thr_3_signal168.777328
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-signal35.189091
Spike_AFFX-r2-Bs-dap_3_signal342.506531
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.579178
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal507.769012
#M346
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.709511
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.047477
Spike_AFFX-r2-Bs-thr_M_signal86.283150
Signal(P)258.874451
Spike_AFFX-r2-Bs-phe_3-5-ratio2.201802
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8322,Count:9
Spike_AFFX-r2-P1-cre_5_signal7120.651367
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9165
Signal(M)17.471554
BackgroundAvg:54.60,Std:0.62,Min:53.6,Max:56.2
Spike_AFFX-r2-Ec-bioC_avg-signal519.822632
Spike_AFFX-r2-Bs-dap_avg-signal210.006882
Spike_AFFX-r2-Bs-dap_3-5-ratio3.585684
Spike_AFFX-r2-Ec-bioB_5_signal138.250626
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.993558
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-2_prt6-1-on-water-agarose_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-2_prt6-1-on-water-agarose_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-2_prt6-1-on-water-agarose_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: prt6-1
Stock Code: N9873
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:1.04446
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-ratio1.130150
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.263627
Spike_AFFX-r2-Bs-dap_5_signal80.230209
NoiseAvg:2.76,Std:0.12,Min:2.4,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.549021
#P13114
Spike_AFFX-r2-Bs-phe_M_signal23.958120
Corner-Avg:14654,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal135.889526
Spike_AFFX-r2-Ec-bioB_3_signal96.921982
Spike_AFFX-r2-Bs-lys_M_signal14.730436
Spike_AFFX-r2-P1-cre_3_signal5349.979980
Spike_AFFX-r2-Bs-lys_3-5-ratio2.104898
Spike_AFFX-r2-Bs-dap_M_signal122.723892
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.780491
Spike_AFFX-r2-Ec-bioB_avg-signal103.170982
Spike_AFFX-r2-Bs-thr_avg-signal52.157383
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1015.289001
Spike_AFFX-r2-Bs-phe_5_signal15.591043
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1355.635620
RawQ2.601552
Spike_AFFX-r2-Bs-lys_5_signal15.859773
Signal(A)5.241895
%A40.863655
Signal(All)148.431519
Corner+Avg:138,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal293.982208
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal42.948978
Spike_AFFX-r2-Ec-bioD_avg-signal1185.462280
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.492329
Spike_AFFX-r2-Bs-lys_avg-signal21.324471
Spike_AFFX-r2-P1-cre_avg-signal5041.922852
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.644016
Spike_AFFX-r2-Bs-thr_3_signal88.673424
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.499380
Spike_AFFX-r2-Bs-dap_3_signal262.041718
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.335221
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal287.509003
#M375
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.383202
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.022515
Spike_AFFX-r2-Bs-thr_M_signal49.249702
Signal(P)253.912598
Spike_AFFX-r2-Bs-phe_3-5-ratio2.754721
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12095,Count:9
Spike_AFFX-r2-P1-cre_5_signal4733.865723
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9321
Signal(M)18.809156
BackgroundAvg:62.43,Std:1.01,Min:60.4,Max:65.6
Spike_AFFX-r2-Ec-bioC_avg-signal290.745605
Spike_AFFX-r2-Bs-dap_avg-signal154.998611
Spike_AFFX-r2-Bs-dap_3-5-ratio3.266123
Spike_AFFX-r2-Ec-bioB_5_signal76.701424
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.044460
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-3_prt6-1-on-water-agarose_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-3_prt6-1-on-water-agarose_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-3_prt6-1-on-water-agarose_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: prt6-1
Stock Code: N9873
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:0.864824
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-ratio1.104331
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.053708
Spike_AFFX-r2-Bs-dap_5_signal88.169746
NoiseAvg:2.58,Std:0.10,Min:2.4,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal33.688953
#P13414
Spike_AFFX-r2-Bs-phe_M_signal20.629541
Corner-Avg:10451,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal148.230560
Spike_AFFX-r2-Ec-bioB_3_signal107.156372
Spike_AFFX-r2-Bs-lys_M_signal19.988529
Spike_AFFX-r2-P1-cre_3_signal5663.915039
Spike_AFFX-r2-Bs-lys_3-5-ratio1.369384
Spike_AFFX-r2-Bs-dap_M_signal151.071350
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.360842
Spike_AFFX-r2-Ec-bioB_avg-signal119.027168
Spike_AFFX-r2-Bs-thr_avg-signal71.728142
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1116.404785
Spike_AFFX-r2-Bs-phe_5_signal22.699322
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1670.153442
RawQ2.588986
Spike_AFFX-r2-Bs-lys_5_signal21.446411
Signal(A)4.161548
%A39.710651
Signal(All)149.433960
Corner+Avg:94,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal406.707520
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.339706
Spike_AFFX-r2-Ec-bioD_avg-signal1393.279053
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.807541
Spike_AFFX-r2-Bs-lys_avg-signal23.601107
Spike_AFFX-r2-P1-cre_avg-signal5396.368164
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal113.223244
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-signal25.222855
Spike_AFFX-r2-Bs-dap_3_signal248.758026
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.496011
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal365.508423
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.368380
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.112717
Spike_AFFX-r2-Bs-thr_M_signal68.272240
Signal(P)250.873123
Spike_AFFX-r2-Bs-phe_3-5-ratio1.424699
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8026,Count:9
Spike_AFFX-r2-P1-cre_5_signal5128.821289
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9058
Signal(M)16.808222
BackgroundAvg:63.74,Std:0.60,Min:62.3,Max:65.3
Spike_AFFX-r2-Ec-bioC_avg-signal386.107971
Spike_AFFX-r2-Bs-dap_avg-signal162.666367
Spike_AFFX-r2-Bs-dap_3-5-ratio2.821353
Spike_AFFX-r2-Ec-bioB_5_signal101.694588
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.864824
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-4_prt6-1-on-water-agarose+ABA_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 ("Nurulhikma_637-4_prt6-1-on-water-agarose+ABA_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-4_prt6-1-on-water-agarose+ABA_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: prt6-1
Stock Code: N9873
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:1.000368
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-ratio1.172942
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.984852
Spike_AFFX-r2-Bs-dap_5_signal86.577080
NoiseAvg:2.49,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_signal15.986010
#P13093
Spike_AFFX-r2-Bs-phe_M_signal19.897327
Corner-Avg:10950,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal159.012253
Spike_AFFX-r2-Ec-bioB_3_signal96.219215
Spike_AFFX-r2-Bs-lys_M_signal25.212662
Spike_AFFX-r2-P1-cre_3_signal6179.201172
Spike_AFFX-r2-Bs-lys_3-5-ratio1.521939
Spike_AFFX-r2-Bs-dap_M_signal151.953262
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.701681
Spike_AFFX-r2-Ec-bioB_avg-signal117.643555
Spike_AFFX-r2-Bs-thr_avg-signal59.331814
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1223.990601
Spike_AFFX-r2-Bs-phe_5_signal8.310634
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1802.975586
RawQ2.500199
Spike_AFFX-r2-Bs-lys_5_signal22.876083
Signal(A)4.721566
%A40.995178
Signal(All)149.318695
Corner+Avg:92,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal430.285797
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal45.728008
Spike_AFFX-r2-Ec-bioD_avg-signal1513.483154
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.400265
Spike_AFFX-r2-Bs-lys_avg-signal27.634912
Spike_AFFX-r2-P1-cre_avg-signal5723.662109
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal91.147125
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-signal24.645323
Spike_AFFX-r2-Bs-dap_3_signal269.028534
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.473031
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal382.318573
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.815998
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.125464
Spike_AFFX-r2-Bs-thr_M_signal70.862305
Signal(P)256.229828
Spike_AFFX-r2-Bs-phe_3-5-ratio5.502349
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8275,Count:9
Spike_AFFX-r2-P1-cre_5_signal5268.123535
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9351
Signal(M)19.101694
BackgroundAvg:61.80,Std:0.59,Min:60.4,Max:63.3
Spike_AFFX-r2-Ec-bioC_avg-signal406.302185
Spike_AFFX-r2-Bs-dap_avg-signal169.186295
Spike_AFFX-r2-Bs-dap_3-5-ratio3.107388
Spike_AFFX-r2-Ec-bioB_5_signal97.699173
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.000368
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-5_prt6-1-on-water-agarose+ABA_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-5_prt6-1-on-water-agarose+ABA_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-5_prt6-1-on-water-agarose+ABA_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: prt6-1
Stock Code: N9873
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:0.731337
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-ratio0.964293
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.996561
Spike_AFFX-r2-Bs-dap_5_signal72.745316
NoiseAvg:2.51,Std:0.05,Min:2.4,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_signal20.908598
#P13585
Spike_AFFX-r2-Bs-phe_M_signal29.076767
Corner-Avg:11781,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal175.834579
Spike_AFFX-r2-Ec-bioB_3_signal110.769920
Spike_AFFX-r2-Bs-lys_M_signal14.188166
Spike_AFFX-r2-P1-cre_3_signal5300.554688
Spike_AFFX-r2-Bs-lys_3-5-ratio2.623123
Spike_AFFX-r2-Bs-dap_M_signal136.574829
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.484289
Spike_AFFX-r2-Ec-bioB_avg-signal132.585571
Spike_AFFX-r2-Bs-thr_avg-signal60.043575
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1091.833618
Spike_AFFX-r2-Bs-phe_5_signal23.959724
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1887.335083
RawQ2.526175
Spike_AFFX-r2-Bs-lys_5_signal10.906708
Signal(A)3.456025
%A38.974133
Signal(All)147.138580
Corner+Avg:114,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal393.679993
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.820621
Spike_AFFX-r2-Ec-bioD_avg-signal1489.584351
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.557213
Spike_AFFX-r2-Bs-lys_avg-signal17.901505
Spike_AFFX-r2-P1-cre_avg-signal5398.693359
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal93.760201
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-signal29.285706
Spike_AFFX-r2-Bs-dap_3_signal228.450638
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.728592
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal363.695801
#M335
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.609640
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.082443
Spike_AFFX-r2-Bs-thr_M_signal65.461922
Signal(P)244.451324
Spike_AFFX-r2-Bs-phe_3-5-ratio1.453298
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8486,Count:9
Spike_AFFX-r2-P1-cre_5_signal5496.831543
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8890
Signal(M)13.837629
BackgroundAvg:61.17,Std:0.53,Min:59.9,Max:62.3
Spike_AFFX-r2-Ec-bioC_avg-signal378.687897
Spike_AFFX-r2-Bs-dap_avg-signal145.923584
Spike_AFFX-r2-Bs-dap_3-5-ratio3.140417
Spike_AFFX-r2-Ec-bioB_5_signal111.152214
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.731337
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-6_prt6-1-on-water-agarose+ABA_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-6_prt6-1-on-water-agarose+ABA_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-6_prt6-1-on-water-agarose+ABA_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: prt6-1
Stock Code: N9873
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:0.715953
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-ratio0.829286
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.192856
Spike_AFFX-r2-Bs-dap_5_signal54.943012
NoiseAvg:2.60,Std:0.09,Min:2.4,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.357787
#P13589
Spike_AFFX-r2-Bs-phe_M_signal17.235140
Corner-Avg:12964,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal150.093735
Spike_AFFX-r2-Ec-bioB_3_signal83.577461
Spike_AFFX-r2-Bs-lys_M_signal14.323118
Spike_AFFX-r2-P1-cre_3_signal3630.060303
Spike_AFFX-r2-Bs-lys_3-5-ratio1.094760
Spike_AFFX-r2-Bs-dap_M_signal149.173691
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.650239
Spike_AFFX-r2-Ec-bioB_avg-signal101.245399
Spike_AFFX-r2-Bs-thr_avg-signal61.621571
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal926.713623
Spike_AFFX-r2-Bs-phe_5_signal20.208035
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1459.685669
RawQ2.535491
Spike_AFFX-r2-Bs-lys_5_signal16.724245
Signal(A)3.431588
%A39.123192
Signal(All)147.864319
Corner+Avg:121,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal298.433502
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.868504
Spike_AFFX-r2-Ec-bioD_avg-signal1193.199707
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.574749
Spike_AFFX-r2-Bs-lys_avg-signal16.452131
Spike_AFFX-r2-P1-cre_avg-signal4003.696777
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.302060
Spike_AFFX-r2-Bs-thr_3_signal102.190269
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-signal25.770559
Spike_AFFX-r2-Bs-dap_3_signal294.195038
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.575121
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal353.729095
#M297
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.309031
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.843678
Spike_AFFX-r2-Bs-thr_M_signal69.316658
Signal(P)245.634521
Spike_AFFX-r2-Bs-phe_3-5-ratio1.972904
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8580,Count:9
Spike_AFFX-r2-P1-cre_5_signal4377.333008
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8924
Signal(M)14.256650
BackgroundAvg:65.56,Std:0.62,Min:63.7,Max:66.9
Spike_AFFX-r2-Ec-bioC_avg-signal326.081299
Spike_AFFX-r2-Bs-dap_avg-signal166.103912
Spike_AFFX-r2-Bs-dap_3-5-ratio5.354549
Spike_AFFX-r2-Ec-bioB_5_signal70.064987
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.715953
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-7_Col-0-on-water-agarose_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 ("Nurulhikma_637-7_Col-0-on-water-agarose_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-7_Col-0-on-water-agarose_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
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:1.476091
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-ratio1.258735
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.162018
Spike_AFFX-r2-Bs-dap_5_signal89.168724
NoiseAvg:1.70,Std:0.04,Min:1.6,Max:1.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.900114
#P13243
Spike_AFFX-r2-Bs-phe_M_signal26.535566
Corner-Avg:8631,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal220.343292
Spike_AFFX-r2-Ec-bioB_3_signal137.807312
Spike_AFFX-r2-Bs-lys_M_signal17.220945
Spike_AFFX-r2-P1-cre_3_signal8831.504883
Spike_AFFX-r2-Bs-lys_3-5-ratio2.748294
Spike_AFFX-r2-Bs-dap_M_signal195.808319
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.841449
Spike_AFFX-r2-Ec-bioB_avg-signal158.914551
Spike_AFFX-r2-Bs-thr_avg-signal107.724243
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1369.434326
Spike_AFFX-r2-Bs-phe_5_signal26.018250
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2267.017822
RawQ1.853038
Spike_AFFX-r2-Bs-lys_5_signal13.264925
Signal(A)5.331900
%A40.302498
Signal(All)154.856674
Corner+Avg:72,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal485.629120
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal60.783890
Spike_AFFX-r2-Ec-bioD_avg-signal1818.226074
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.057869
Spike_AFFX-r2-Bs-lys_avg-signal22.313929
Spike_AFFX-r2-P1-cre_avg-signal7923.838867
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.639632
Spike_AFFX-r2-Bs-thr_3_signal220.153091
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-signal37.779236
Spike_AFFX-r2-Bs-dap_3_signal326.420135
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.655441
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal443.869354
#M374
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.455917
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.094081
Spike_AFFX-r2-Bs-thr_M_signal78.119530
Signal(P)262.433014
Spike_AFFX-r2-Bs-phe_3-5-ratio2.336202
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6132,Count:9
Spike_AFFX-r2-P1-cre_5_signal7016.172852
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9193
Signal(M)21.027840
BackgroundAvg:45.80,Std:0.18,Min:45.2,Max:46.2
Spike_AFFX-r2-Ec-bioC_avg-signal464.749237
Spike_AFFX-r2-Bs-dap_avg-signal203.799057
Spike_AFFX-r2-Bs-dap_3-5-ratio3.660702
Spike_AFFX-r2-Ec-bioB_5_signal118.593048
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.476091
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-8_Col-0-on-water-agarose_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-8_Col-0-on-water-agarose_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-8_Col-0-on-water-agarose_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
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:0.746774
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-ratio1.128520
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.977394
Spike_AFFX-r2-Bs-dap_5_signal60.594963
NoiseAvg:2.72,Std:0.14,Min:2.4,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.210793
#P13623
Spike_AFFX-r2-Bs-phe_M_signal20.485954
Corner-Avg:11592,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal134.889297
Spike_AFFX-r2-Ec-bioB_3_signal87.086800
Spike_AFFX-r2-Bs-lys_M_signal11.065077
Spike_AFFX-r2-P1-cre_3_signal5248.706543
Spike_AFFX-r2-Bs-lys_3-5-ratio1.320254
Spike_AFFX-r2-Bs-dap_M_signal98.108505
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.939544
Spike_AFFX-r2-Ec-bioB_avg-signal103.692383
Spike_AFFX-r2-Bs-thr_avg-signal48.608913
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal887.201172
Spike_AFFX-r2-Bs-phe_5_signal17.029722
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1461.000732
RawQ2.460203
Spike_AFFX-r2-Bs-lys_5_signal16.584488
Signal(A)4.361491
%A38.667252
Signal(All)151.062531
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal372.283173
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal40.738014
Spike_AFFX-r2-Ec-bioD_avg-signal1174.100952
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.723804
Spike_AFFX-r2-Bs-lys_avg-signal16.515100
Spike_AFFX-r2-P1-cre_avg-signal4949.835938
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal65.289604
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.084564
Spike_AFFX-r2-Bs-dap_3_signal206.828918
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.646752
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal338.106903
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.895737
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.101081
Spike_AFFX-r2-Bs-thr_M_signal58.326340
Signal(P)249.684174
Spike_AFFX-r2-Bs-phe_3-5-ratio2.392171
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9793,Count:9
Spike_AFFX-r2-P1-cre_5_signal4650.965332
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8820
Signal(M)15.859509
BackgroundAvg:62.38,Std:0.66,Min:60.4,Max:63.8
Spike_AFFX-r2-Ec-bioC_avg-signal355.195038
Spike_AFFX-r2-Bs-dap_avg-signal121.844139
Spike_AFFX-r2-Bs-dap_3-5-ratio3.413302
Spike_AFFX-r2-Ec-bioB_5_signal89.101036
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.746774
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-9_Col-0-on-water-agarose_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-9_Col-0-on-water-agarose_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-9_Col-0-on-water-agarose_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
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:0.903304
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-ratio1.136219
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.959311
Spike_AFFX-r2-Bs-dap_5_signal39.876762
NoiseAvg:2.58,Std:0.06,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_signal12.810969
#P13205
Spike_AFFX-r2-Bs-phe_M_signal11.028239
Corner-Avg:11181,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal127.875511
Spike_AFFX-r2-Ec-bioB_3_signal75.698349
Spike_AFFX-r2-Bs-lys_M_signal7.859855
Spike_AFFX-r2-P1-cre_3_signal5364.780273
Spike_AFFX-r2-Bs-lys_3-5-ratio2.280805
Spike_AFFX-r2-Bs-dap_M_signal67.845596
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.339035
Spike_AFFX-r2-Ec-bioB_avg-signal94.160980
Spike_AFFX-r2-Bs-thr_avg-signal35.494762
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal868.393555
Spike_AFFX-r2-Bs-phe_5_signal12.386125
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1515.434326
RawQ2.516658
Spike_AFFX-r2-Bs-lys_5_signal6.206517
Signal(A)4.795788
%A40.442787
Signal(All)152.501312
Corner+Avg:107,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal347.352142
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.764793
Spike_AFFX-r2-Ec-bioD_avg-signal1191.913940
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.891277
Spike_AFFX-r2-Bs-lys_avg-signal9.407409
Spike_AFFX-r2-P1-cre_avg-signal5043.193359
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.665936
Spike_AFFX-r2-Bs-thr_3_signal55.587246
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal15.059719
Spike_AFFX-r2-Bs-dap_3_signal150.901917
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.745101
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal335.084259
#M380
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.155854
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.036611
Spike_AFFX-r2-Bs-thr_M_signal38.086075
Signal(P)259.555908
Spike_AFFX-r2-Bs-phe_3-5-ratio1.757192
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8720,Count:9
Spike_AFFX-r2-P1-cre_5_signal4721.606445
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9225
Signal(M)18.100050
BackgroundAvg:62.01,Std:0.44,Min:61.1,Max:63.4
Spike_AFFX-r2-Ec-bioC_avg-signal341.218201
Spike_AFFX-r2-Bs-dap_avg-signal86.208092
Spike_AFFX-r2-Bs-dap_3-5-ratio3.784207
Spike_AFFX-r2-Ec-bioB_5_signal78.909096
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.903304
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-10_Col-0-on-water-agarose+ABA_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 ("Nurulhikma_637-10_Col-0-on-water-agarose+ABA_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-10_Col-0-on-water-agarose+ABA_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
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:1.077067
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-ratio1.054449
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.828494
Spike_AFFX-r2-Bs-dap_5_signal52.778782
NoiseAvg:2.00,Std:0.10,Min:1.8,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.289968
#P13244
Spike_AFFX-r2-Bs-phe_M_signal17.295242
Corner-Avg:10394,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal188.537888
Spike_AFFX-r2-Ec-bioB_3_signal101.274963
Spike_AFFX-r2-Bs-lys_M_signal14.097182
Spike_AFFX-r2-P1-cre_3_signal7413.354980
Spike_AFFX-r2-Bs-lys_3-5-ratio1.572903
Spike_AFFX-r2-Bs-dap_M_signal128.398636
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.563793
Spike_AFFX-r2-Ec-bioB_avg-signal137.350876
Spike_AFFX-r2-Bs-thr_avg-signal48.035049
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1491.442261
Spike_AFFX-r2-Bs-phe_5_signal11.680621
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2237.776367
RawQ2.163904
Spike_AFFX-r2-Bs-lys_5_signal10.666891
Signal(A)4.288153
%A40.718983
Signal(All)150.209305
Corner+Avg:102,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal457.855499
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.901430
Spike_AFFX-r2-Ec-bioD_avg-signal1864.609375
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P58.062252
Spike_AFFX-r2-Bs-lys_avg-signal13.847351
Spike_AFFX-r2-P1-cre_avg-signal7221.951172
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.218764
Spike_AFFX-r2-Bs-thr_3_signal87.232605
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.625765
Spike_AFFX-r2-Bs-dap_3_signal204.975754
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.500411
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal466.920654
#M278
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.777981
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.980585
Spike_AFFX-r2-Bs-thr_M_signal43.582581
Signal(P)255.321487
Spike_AFFX-r2-Bs-phe_3-5-ratio2.559918
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6653,Count:9
Spike_AFFX-r2-P1-cre_5_signal7030.547852
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9288
Signal(M)17.871128
BackgroundAvg:73.08,Std:0.65,Min:72.0,Max:74.6
Spike_AFFX-r2-Ec-bioC_avg-signal462.388062
Spike_AFFX-r2-Bs-dap_avg-signal128.717728
Spike_AFFX-r2-Bs-dap_3-5-ratio3.883677
Spike_AFFX-r2-Ec-bioB_5_signal122.239777
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.077067
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-11_Col-0-on-water-agarose+ABA_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-11_Col-0-on-water-agarose+ABA_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-11_Col-0-on-water-agarose+ABA_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
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:1.321757
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-ratio0.998911
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.958606
Spike_AFFX-r2-Bs-dap_5_signal52.799534
NoiseAvg:2.32,Std:0.09,Min:2.1,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_signal19.668692
#P12619
Spike_AFFX-r2-Bs-phe_M_signal17.426149
Corner-Avg:8790,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal159.718491
Spike_AFFX-r2-Ec-bioB_3_signal99.179497
Spike_AFFX-r2-Bs-lys_M_signal11.659607
Spike_AFFX-r2-P1-cre_3_signal5869.056641
Spike_AFFX-r2-Bs-lys_3-5-ratio2.765731
Spike_AFFX-r2-Bs-dap_M_signal102.041176
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.794156
Spike_AFFX-r2-Ec-bioB_avg-signal120.786713
Spike_AFFX-r2-Bs-thr_avg-signal45.836254
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1059.074585
Spike_AFFX-r2-Bs-phe_5_signal12.482359
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1679.186035
RawQ2.418818
Spike_AFFX-r2-Bs-lys_5_signal12.791018
Signal(A)5.909338
%A43.020603
Signal(All)149.704056
Corner+Avg:74,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal377.979462
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.258583
Spike_AFFX-r2-Ec-bioD_avg-signal1369.130371
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P55.322227
Spike_AFFX-r2-Bs-lys_avg-signal19.942381
Spike_AFFX-r2-P1-cre_avg-signal5872.255371
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.657168
Spike_AFFX-r2-Bs-thr_3_signal74.626076
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.389030
Spike_AFFX-r2-Bs-dap_3_signal207.516373
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.585522
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal411.872223
#M378
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.376518
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.917710
Spike_AFFX-r2-Bs-thr_M_signal43.213993
Signal(P)265.324219
Spike_AFFX-r2-Bs-phe_3-5-ratio2.744560
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6488,Count:9
Spike_AFFX-r2-P1-cre_5_signal5875.454102
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9813
Signal(M)22.842701
BackgroundAvg:80.92,Std:0.77,Min:79.3,Max:82.7
Spike_AFFX-r2-Ec-bioC_avg-signal394.925842
Spike_AFFX-r2-Bs-dap_avg-signal120.785698
Spike_AFFX-r2-Bs-dap_3-5-ratio3.930269
Spike_AFFX-r2-Ec-bioB_5_signal103.462158
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.321757
NF1.000000
HZ4
Tau0.015000

Slide: Nurulhikma_637-12_Col-0-on-water-agarose+ABA_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Nurulhikma_637-12_Col-0-on-water-agarose+ABA_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Nurulhikma_637-12_Col-0-on-water-agarose+ABA_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
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:1.038274
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-ratio0.950638
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.019830
Spike_AFFX-r2-Bs-dap_5_signal59.485123
NoiseAvg:2.20,Std:0.08,Min:2.0,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.117104
#P13264
Spike_AFFX-r2-Bs-phe_M_signal27.039726
Corner-Avg:11172,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal118.466972
Spike_AFFX-r2-Ec-bioB_3_signal83.804741
Spike_AFFX-r2-Bs-lys_M_signal18.517231
Spike_AFFX-r2-P1-cre_3_signal4330.539063
Spike_AFFX-r2-Bs-lys_3-5-ratio1.538365
Spike_AFFX-r2-Bs-dap_M_signal102.969719
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.269474
Spike_AFFX-r2-Ec-bioB_avg-signal94.815636
Spike_AFFX-r2-Bs-thr_avg-signal57.069103
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1102.508667
Spike_AFFX-r2-Bs-phe_5_signal13.923982
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1849.737427
RawQ2.291972
Spike_AFFX-r2-Bs-lys_5_signal12.070346
Signal(A)4.414738
%A40.460323
Signal(All)149.756836
Corner+Avg:86,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal315.322479
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.380049
Spike_AFFX-r2-Ec-bioD_avg-signal1476.123047
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.149933
Spike_AFFX-r2-Bs-lys_avg-signal16.385391
Spike_AFFX-r2-P1-cre_avg-signal4442.969727
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.389741
Spike_AFFX-r2-Bs-thr_3_signal84.928658
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.781252
Spike_AFFX-r2-Bs-dap_3_signal226.448868
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.677753
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal268.743439
#M317
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.568596
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.173322
Spike_AFFX-r2-Bs-thr_M_signal70.161560
Signal(P)254.026932
Spike_AFFX-r2-Bs-phe_3-5-ratio2.181851
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8992,Count:9
Spike_AFFX-r2-P1-cre_5_signal4555.400879
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9229
Signal(M)18.285513
BackgroundAvg:78.65,Std:0.52,Min:76.9,Max:79.8
Spike_AFFX-r2-Ec-bioC_avg-signal292.032959
Spike_AFFX-r2-Bs-dap_avg-signal129.634567
Spike_AFFX-r2-Bs-dap_3-5-ratio3.806815
Spike_AFFX-r2-Ec-bioB_5_signal82.175171
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.038274
NF1.000000
HZ4
Tau0.015000


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