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Experiment: Fenclorim safening of Arabidopsis

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-494

Wildtype arabidopsis thaliana Col-0 root cultures, were treated with fenclorim or 4-chloro-6-methyl-2-phenylpyrimidine dissolved in acetone to achieve a final concentration of 100uM. The final acetone concentration of 0.1% was replicated in control root cultures. Samples were taken at four and twenty-four hours post addition in biological triplicate. Root cultures were routinely maintained at 25oC in the dark.

About the Experimenter

Name:Dr Mark Skipsey
Head of Lab Name:Prof Robert Edwards
Lab:
Address:Durham University
School of Biological and Biomedical Sciences
University Science Laboratories
South Road
Durham
Postcode: DH1 3LE
Country: UK
 
Telephone Number: 01913342143

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: time_series_design; compound_treatment_design
Number of Slides:18
 
Experimental Parameters:
parametertimepoint
parametercompound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Skipsey: Fenclorim safening of Arabidopsis_genome

Slide: Skipsey_1-8_Fenclorim_4hr_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("Skipsey_1-8_Fenclorim_4hr_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: Skipsey_1-8_Fenclorim_4hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Secondly the safener compound fenclorim was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.430902
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-ratio1.233045
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.285433
Spike_AFFX-r2-Bs-dap_5_signal219.316757
NoiseAvg:2.92,Std:0.05,Min:2.8,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal52.571030
#P15059
Spike_AFFX-r2-Bs-phe_M_signal73.220139
Corner-Avg:13784,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.258400
Spike_AFFX-r2-Ec-bioB_3_signal75.256096
Spike_AFFX-r2-Bs-lys_M_signal36.697330
Spike_AFFX-r2-P1-cre_3_signal4221.984375
Spike_AFFX-r2-Bs-lys_3-5-ratio1.085684
Spike_AFFX-r2-Bs-dap_M_signal381.490631
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.471827
Spike_AFFX-r2-Ec-bioB_avg-signal74.686607
Spike_AFFX-r2-Bs-thr_avg-signal145.252060
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal695.537598
Spike_AFFX-r2-Bs-phe_5_signal115.746185
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1078.618408
RawQ2.540191
Spike_AFFX-r2-Bs-lys_5_signal43.492126
Signal(A)3.169852
%A32.332310
Signal(All)138.820435
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal272.009186
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal106.365913
Spike_AFFX-r2-Ec-bioD_avg-signal887.078003
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.019287
Spike_AFFX-r2-Bs-lys_avg-signal42.469391
Spike_AFFX-r2-P1-cre_avg-signal3823.008057
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.648400
Spike_AFFX-r2-Bs-thr_3_signal235.088547
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-signal98.444084
Spike_AFFX-r2-Bs-dap_3_signal515.430298
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.550769
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.800308
#M376
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.218719
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.134315
Spike_AFFX-r2-Bs-thr_M_signal148.096573
Signal(P)208.428177
Spike_AFFX-r2-Bs-phe_3-5-ratio0.918958
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11986,Count:9
Spike_AFFX-r2-P1-cre_5_signal3424.031738
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7375
Signal(M)11.692400
BackgroundAvg:66.92,Std:0.57,Min:65.1,Max:68.4
Spike_AFFX-r2-Ec-bioC_avg-signal255.904755
Spike_AFFX-r2-Bs-dap_avg-signal372.079224
Spike_AFFX-r2-Bs-dap_3-5-ratio2.350164
Spike_AFFX-r2-Ec-bioB_5_signal58.545338
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.430902
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-7_Fenclorim_4hr_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 ("Skipsey_1-7_Fenclorim_4hr_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: Skipsey_1-7_Fenclorim_4hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Secondly the safener compound fenclorim was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.532485
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-ratio1.147714
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.136621
Spike_AFFX-r2-Bs-dap_5_signal241.684464
NoiseAvg:2.88,Std:0.08,Min:2.7,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_signal79.105217
#P14732
Spike_AFFX-r2-Bs-phe_M_signal92.828773
Corner-Avg:14951,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal108.926605
Spike_AFFX-r2-Ec-bioB_3_signal68.395393
Spike_AFFX-r2-Bs-lys_M_signal46.667549
Spike_AFFX-r2-P1-cre_3_signal4018.495850
Spike_AFFX-r2-Bs-lys_3-5-ratio1.091916
Spike_AFFX-r2-Bs-dap_M_signal434.553131
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.990610
Spike_AFFX-r2-Ec-bioB_avg-signal79.165443
Spike_AFFX-r2-Bs-thr_avg-signal200.865494
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal734.880188
Spike_AFFX-r2-Bs-phe_5_signal148.975311
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1274.289673
RawQ2.612626
Spike_AFFX-r2-Bs-lys_5_signal52.137257
Signal(A)4.007245
%A33.717667
Signal(All)139.700546
Corner+Avg:123,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal293.321655
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal126.728043
Spike_AFFX-r2-Ec-bioD_avg-signal1004.584961
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.585709
Spike_AFFX-r2-Bs-lys_avg-signal51.911438
Spike_AFFX-r2-P1-cre_avg-signal3759.900391
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.696624
Spike_AFFX-r2-Bs-thr_3_signal315.678040
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-signal122.844048
Spike_AFFX-r2-Bs-dap_3_signal569.226074
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.734010
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal254.505402
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.929512
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.152516
Spike_AFFX-r2-Bs-thr_M_signal207.813217
Signal(P)213.858337
Spike_AFFX-r2-Bs-phe_3-5-ratio0.850665
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11210,Count:9
Spike_AFFX-r2-P1-cre_5_signal3501.304932
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7691
Signal(M)13.407242
BackgroundAvg:66.44,Std:0.71,Min:64.6,Max:68.1
Spike_AFFX-r2-Ec-bioC_avg-signal273.913513
Spike_AFFX-r2-Bs-dap_avg-signal415.154541
Spike_AFFX-r2-Bs-dap_3-5-ratio2.355245
Spike_AFFX-r2-Ec-bioB_5_signal60.174328
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.532485
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-6_Acetone_24hr_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 ("Skipsey_1-6_Acetone_24hr_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: Skipsey_1-6_Acetone_24hr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe inducing chemical treatments were prepared as 100 mM stocks in acetone and added to the medium as a 1:1000 dilution. Control treatments consisted of 0.1% v/v acetone. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.412389
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-ratio1.202875
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.621202
Spike_AFFX-r2-Bs-dap_5_signal100.874619
NoiseAvg:3.24,Std:0.12,Min:3.0,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal34.310131
#P15264
Spike_AFFX-r2-Bs-phe_M_signal45.265789
Corner-Avg:14651,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal60.373390
Spike_AFFX-r2-Ec-bioB_3_signal52.512356
Spike_AFFX-r2-Bs-lys_M_signal24.054058
Spike_AFFX-r2-P1-cre_3_signal3493.252930
Spike_AFFX-r2-Bs-lys_3-5-ratio1.774279
Spike_AFFX-r2-Bs-dap_M_signal208.050858
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.139200
Spike_AFFX-r2-Ec-bioB_avg-signal48.425579
Spike_AFFX-r2-Bs-thr_avg-signal75.211494
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal659.865417
Spike_AFFX-r2-Bs-phe_5_signal44.612144
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal965.210449
RawQ2.493705
Spike_AFFX-r2-Bs-lys_5_signal25.002192
Signal(A)4.596787
%A31.139851
Signal(All)136.522003
Corner+Avg:138,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal199.109985
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.845951
Spike_AFFX-r2-Ec-bioD_avg-signal812.537964
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.918022
Spike_AFFX-r2-Bs-lys_avg-signal31.139036
Spike_AFFX-r2-P1-cre_avg-signal3198.670410
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.942131
Spike_AFFX-r2-Bs-thr_3_signal107.706352
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-signal50.907959
Spike_AFFX-r2-Bs-dap_3_signal333.071808
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.462738
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal177.115311
#M443
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.360859
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.124183
Spike_AFFX-r2-Bs-thr_M_signal83.617989
Signal(P)201.403259
Spike_AFFX-r2-Bs-phe_3-5-ratio1.408718
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11309,Count:9
Spike_AFFX-r2-P1-cre_5_signal2904.087646
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7103
Signal(M)16.245144
BackgroundAvg:66.97,Std:0.87,Min:64.2,Max:68.5
Spike_AFFX-r2-Ec-bioC_avg-signal188.112640
Spike_AFFX-r2-Bs-dap_avg-signal213.999100
Spike_AFFX-r2-Bs-dap_3-5-ratio3.301840
Spike_AFFX-r2-Ec-bioB_5_signal32.390999
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.412389
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-5_Acetone_24hr_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Skipsey_1-5_Acetone_24hr_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: Skipsey_1-5_Acetone_24hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe inducing chemical treatments were prepared as 100 mM stocks in acetone and added to the medium as a 1:1000 dilution. Control treatments consisted of 0.1% v/v acetone. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.513944
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-ratio1.148265
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.063280
Spike_AFFX-r2-Bs-dap_5_signal182.977829
NoiseAvg:3.35,Std:0.10,Min:3.0,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal78.982735
#P15483
Spike_AFFX-r2-Bs-phe_M_signal65.874451
Corner-Avg:11936,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal70.604561
Spike_AFFX-r2-Ec-bioB_3_signal58.058990
Spike_AFFX-r2-Bs-lys_M_signal26.458292
Spike_AFFX-r2-P1-cre_3_signal3250.592041
Spike_AFFX-r2-Bs-lys_3-5-ratio1.306093
Spike_AFFX-r2-Bs-dap_M_signal324.028839
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.391049
Spike_AFFX-r2-Ec-bioB_avg-signal61.089066
Spike_AFFX-r2-Bs-thr_avg-signal173.283997
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal565.886230
Spike_AFFX-r2-Bs-phe_5_signal90.663574
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal858.629944
RawQ2.902538
Spike_AFFX-r2-Bs-lys_5_signal41.102852
Signal(A)4.455141
%A30.574310
Signal(All)134.771240
Corner+Avg:102,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal208.224899
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal127.683105
Spike_AFFX-r2-Ec-bioD_avg-signal712.258057
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.878120
Spike_AFFX-r2-Bs-lys_avg-signal40.415092
Spike_AFFX-r2-P1-cre_avg-signal3040.731934
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_signal267.834320
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-signal94.740379
Spike_AFFX-r2-Bs-dap_3_signal481.707062
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.517319
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal192.017578
#M353
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.684132
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.084405
Spike_AFFX-r2-Bs-thr_M_signal173.034927
Signal(P)196.178162
Spike_AFFX-r2-Bs-phe_3-5-ratio1.408318
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6013,Count:9
Spike_AFFX-r2-P1-cre_5_signal2830.871582
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6974
Signal(M)15.964540
BackgroundAvg:76.07,Std:0.71,Min:74.4,Max:77.9
Spike_AFFX-r2-Ec-bioC_avg-signal200.121246
Spike_AFFX-r2-Bs-dap_avg-signal329.571259
Spike_AFFX-r2-Bs-dap_3-5-ratio2.632598
Spike_AFFX-r2-Ec-bioB_5_signal54.603653
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.513944
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-4_Acetone_24hr_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 ("Skipsey_1-4_Acetone_24hr_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: Skipsey_1-4_Acetone_24hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe inducing chemical treatments were prepared as 100 mM stocks in acetone and added to the medium as a 1:1000 dilution. Control treatments consisted of 0.1% v/v acetone. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.485127
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-ratio1.129067
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.000207
Spike_AFFX-r2-Bs-dap_5_signal245.972351
NoiseAvg:3.42,Std:0.15,Min:3.1,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal93.357407
#P15829
Spike_AFFX-r2-Bs-phe_M_signal90.800194
Corner-Avg:14925,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal107.929039
Spike_AFFX-r2-Ec-bioB_3_signal75.242798
Spike_AFFX-r2-Bs-lys_M_signal37.138016
Spike_AFFX-r2-P1-cre_3_signal4332.500488
Spike_AFFX-r2-Bs-lys_3-5-ratio0.955728
Spike_AFFX-r2-Bs-dap_M_signal438.516266
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.982649
Spike_AFFX-r2-Ec-bioB_avg-signal86.133026
Spike_AFFX-r2-Bs-thr_avg-signal193.613220
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal881.306396
Spike_AFFX-r2-Bs-phe_5_signal104.853500
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1268.552734
RawQ2.906680
Spike_AFFX-r2-Bs-lys_5_signal57.192818
Signal(A)3.453758
%A29.263481
Signal(All)136.049194
Corner+Avg:130,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal291.585236
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal123.693672
Spike_AFFX-r2-Ec-bioD_avg-signal1074.929565
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.395004
Spike_AFFX-r2-Bs-lys_avg-signal49.663868
Spike_AFFX-r2-P1-cre_avg-signal4084.870361
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.341517
Spike_AFFX-r2-Bs-thr_3_signal278.452332
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-signal106.449120
Spike_AFFX-r2-Bs-dap_3_signal607.963562
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.439400
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal262.295563
#M306
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal54.660786
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.111667
Spike_AFFX-r2-Bs-thr_M_signal209.029892
Signal(P)194.343857
Spike_AFFX-r2-Bs-phe_3-5-ratio1.179681
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12007,Count:9
Spike_AFFX-r2-P1-cre_5_signal3837.240234
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6675
Signal(M)12.938626
BackgroundAvg:78.45,Std:0.79,Min:76.5,Max:80.5
Spike_AFFX-r2-Ec-bioC_avg-signal276.940399
Spike_AFFX-r2-Bs-dap_avg-signal430.817383
Spike_AFFX-r2-Bs-dap_3-5-ratio2.471674
Spike_AFFX-r2-Ec-bioB_5_signal75.227226
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.485127
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-3_Acetone_4hr_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 ("Skipsey_1-3_Acetone_4hr_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: Skipsey_1-3_Acetone_4hr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe inducing chemical treatments were prepared as 100 mM stocks in acetone and added to the medium as a 1:1000 dilution. Control treatments consisted of 0.1% v/v acetone. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.524793
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-ratio1.321254
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.974485
Spike_AFFX-r2-Bs-dap_5_signal205.691513
NoiseAvg:2.99,Std:0.07,Min:2.7,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_signal69.871315
#P15502
Spike_AFFX-r2-Bs-phe_M_signal68.165710
Corner-Avg:13656,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.491241
Spike_AFFX-r2-Ec-bioB_3_signal60.221115
Spike_AFFX-r2-Bs-lys_M_signal34.007092
Spike_AFFX-r2-P1-cre_3_signal3806.360352
Spike_AFFX-r2-Bs-lys_3-5-ratio1.248277
Spike_AFFX-r2-Bs-dap_M_signal325.763031
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.374749
Spike_AFFX-r2-Ec-bioB_avg-signal67.836754
Spike_AFFX-r2-Bs-thr_avg-signal147.335373
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal729.703491
Spike_AFFX-r2-Bs-phe_5_signal84.272682
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1004.453125
RawQ2.679375
Spike_AFFX-r2-Bs-lys_5_signal41.667213
Signal(A)4.073766
%A30.552389
Signal(All)136.674805
Corner+Avg:118,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal214.864716
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.365322
Spike_AFFX-r2-Ec-bioD_avg-signal867.078308
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.961418
Spike_AFFX-r2-Bs-lys_avg-signal42.562183
Spike_AFFX-r2-P1-cre_avg-signal3343.614746
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.486190
Spike_AFFX-r2-Bs-thr_3_signal235.798157
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal71.601234
Spike_AFFX-r2-Bs-dap_3_signal355.209991
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.376522
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal236.902115
#M339
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal52.012241
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.906977
Spike_AFFX-r2-Bs-thr_M_signal136.336685
Signal(P)198.958115
Spike_AFFX-r2-Bs-phe_3-5-ratio0.740042
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9162,Count:9
Spike_AFFX-r2-P1-cre_5_signal2880.869385
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6969
Signal(M)14.494462
BackgroundAvg:79.31,Std:0.53,Min:77.6,Max:80.3
Spike_AFFX-r2-Ec-bioC_avg-signal225.883423
Spike_AFFX-r2-Bs-dap_avg-signal295.554840
Spike_AFFX-r2-Bs-dap_3-5-ratio1.726906
Spike_AFFX-r2-Ec-bioB_5_signal61.797909
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.524793
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-2_Acetone_4hr_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Skipsey_1-2_Acetone_4hr_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: Skipsey_1-2_Acetone_4hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe inducing chemical treatments were prepared as 100 mM stocks in acetone and added to the medium as a 1:1000 dilution. Control treatments consisted of 0.1% v/v acetone. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.459892
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-ratio1.137000
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.559959
Spike_AFFX-r2-Bs-dap_5_signal112.631836
NoiseAvg:3.16,Std:0.08,Min:2.9,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_signal41.112377
#P15241
Spike_AFFX-r2-Bs-phe_M_signal53.468681
Corner-Avg:13778,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.204926
Spike_AFFX-r2-Ec-bioB_3_signal65.868568
Spike_AFFX-r2-Bs-lys_M_signal21.232611
Spike_AFFX-r2-P1-cre_3_signal3205.619873
Spike_AFFX-r2-Bs-lys_3-5-ratio1.448087
Spike_AFFX-r2-Bs-dap_M_signal212.862305
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.559755
Spike_AFFX-r2-Ec-bioB_avg-signal61.099346
Spike_AFFX-r2-Bs-thr_avg-signal98.610466
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal605.099060
Spike_AFFX-r2-Bs-phe_5_signal55.873344
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal963.437317
RawQ2.835086
Spike_AFFX-r2-Bs-lys_5_signal28.601625
Signal(A)3.982758
%A31.543182
Signal(All)138.342728
Corner+Avg:116,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal218.568954
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal68.446526
Spike_AFFX-r2-Ec-bioD_avg-signal784.268188
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.817184
Spike_AFFX-r2-Bs-lys_avg-signal30.417295
Spike_AFFX-r2-P1-cre_avg-signal3012.493408
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_signal146.349991
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-signal59.262848
Spike_AFFX-r2-Bs-dap_3_signal312.447418
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.592198
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal194.569382
#M374
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.417652
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.123347
Spike_AFFX-r2-Bs-thr_M_signal108.369026
Signal(P)204.779541
Spike_AFFX-r2-Bs-phe_3-5-ratio1.225030
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10941,Count:9
Spike_AFFX-r2-P1-cre_5_signal2819.366943
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7195
Signal(M)15.766478
BackgroundAvg:79.50,Std:0.63,Min:78.1,Max:80.7
Spike_AFFX-r2-Ec-bioC_avg-signal206.569168
Spike_AFFX-r2-Bs-dap_avg-signal212.647171
Spike_AFFX-r2-Bs-dap_3-5-ratio2.774060
Spike_AFFX-r2-Ec-bioB_5_signal42.224541
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.459892
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-1_Acetone_4hr_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 ("Skipsey_1-1_Acetone_4hr_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: Skipsey_1-1_Acetone_4hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe inducing chemical treatments were prepared as 100 mM stocks in acetone and added to the medium as a 1:1000 dilution. Control treatments consisted of 0.1% v/v acetone. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.578829
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-ratio1.145372
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.013459
Spike_AFFX-r2-Bs-dap_5_signal132.565735
NoiseAvg:3.08,Std:0.16,Min:2.6,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal47.358257
#P15211
Spike_AFFX-r2-Bs-phe_M_signal55.702755
Corner-Avg:13465,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.724945
Spike_AFFX-r2-Ec-bioB_3_signal58.611919
Spike_AFFX-r2-Bs-lys_M_signal20.219429
Spike_AFFX-r2-P1-cre_3_signal3301.135986
Spike_AFFX-r2-Bs-lys_3-5-ratio1.535815
Spike_AFFX-r2-Bs-dap_M_signal205.972000
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.219962
Spike_AFFX-r2-Ec-bioB_avg-signal66.723457
Spike_AFFX-r2-Bs-thr_avg-signal122.347290
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal660.638062
Spike_AFFX-r2-Bs-phe_5_signal53.019920
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal952.246704
RawQ2.745474
Spike_AFFX-r2-Bs-lys_5_signal29.542133
Signal(A)4.193978
%A31.762384
Signal(All)137.174789
Corner+Avg:117,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.356003
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal83.543076
Spike_AFFX-r2-Ec-bioD_avg-signal806.442383
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.685661
Spike_AFFX-r2-Bs-lys_avg-signal31.710938
Spike_AFFX-r2-P1-cre_avg-signal3091.644043
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.551951
Spike_AFFX-r2-Bs-thr_3_signal199.850037
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-signal64.088585
Spike_AFFX-r2-Bs-dap_3_signal318.522766
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.441405
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal211.255127
#M354
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.371246
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.972076
Spike_AFFX-r2-Bs-thr_M_signal119.833595
Signal(P)203.314453
Spike_AFFX-r2-Bs-phe_3-5-ratio1.575692
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10695,Count:9
Spike_AFFX-r2-P1-cre_5_signal2882.152100
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7245
Signal(M)16.823309
BackgroundAvg:66.80,Std:0.94,Min:64.1,Max:69.1
Spike_AFFX-r2-Ec-bioC_avg-signal208.305573
Spike_AFFX-r2-Bs-dap_avg-signal219.020157
Spike_AFFX-r2-Bs-dap_3-5-ratio2.402753
Spike_AFFX-r2-Ec-bioB_5_signal57.833519
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.578829
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-9_Fenclorim_4hr_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 ("Skipsey_1-9_Fenclorim_4hr_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: Skipsey_1-9_Fenclorim_4hr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Secondly the safener compound fenclorim was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.543273
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-ratio1.133511
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.987415
Spike_AFFX-r2-Bs-dap_5_signal313.745483
NoiseAvg:2.76,Std:0.11,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_signal108.553558
#P14760
Spike_AFFX-r2-Bs-phe_M_signal106.450027
Corner-Avg:14664,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal118.010033
Spike_AFFX-r2-Ec-bioB_3_signal89.017876
Spike_AFFX-r2-Bs-lys_M_signal52.654739
Spike_AFFX-r2-P1-cre_3_signal4510.378418
Spike_AFFX-r2-Bs-lys_3-5-ratio1.076616
Spike_AFFX-r2-Bs-dap_M_signal583.861389
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.746832
Spike_AFFX-r2-Ec-bioB_avg-signal99.060120
Spike_AFFX-r2-Bs-thr_avg-signal199.542358
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal753.829956
Spike_AFFX-r2-Bs-phe_5_signal148.984116
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1254.618530
RawQ2.537987
Spike_AFFX-r2-Bs-lys_5_signal77.995750
Signal(A)3.689480
%A33.445858
Signal(All)142.013290
Corner+Avg:122,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal288.611786
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal135.862839
Spike_AFFX-r2-Ec-bioD_avg-signal1004.224243
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.708458
Spike_AFFX-r2-Bs-lys_avg-signal71.540672
Spike_AFFX-r2-P1-cre_avg-signal4244.750000
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.845682
Spike_AFFX-r2-Bs-thr_3_signal298.178436
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-signal130.432327
Spike_AFFX-r2-Bs-dap_3_signal843.885742
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.664326
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal268.700684
#M421
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal83.971504
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.074101
Spike_AFFX-r2-Bs-thr_M_signal191.895050
Signal(P)217.162140
Spike_AFFX-r2-Bs-phe_3-5-ratio0.911928
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11251,Count:9
Spike_AFFX-r2-P1-cre_5_signal3979.121582
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7629
Signal(M)13.925840
BackgroundAvg:60.99,Std:0.45,Min:60.0,Max:62.6
Spike_AFFX-r2-Ec-bioC_avg-signal278.656250
Spike_AFFX-r2-Bs-dap_avg-signal580.497498
Spike_AFFX-r2-Bs-dap_3-5-ratio2.689714
Spike_AFFX-r2-Ec-bioB_5_signal90.152466
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.543273
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-10_Fenclorim_24hr_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Skipsey_1-10_Fenclorim_24hr_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: Skipsey_1-10_Fenclorim_24hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Secondly the safener compound fenclorim was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.754861
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-ratio1.213117
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.083619
Spike_AFFX-r2-Bs-dap_5_signal385.268494
NoiseAvg:2.76,Std:0.08,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal144.764816
#P13652
Spike_AFFX-r2-Bs-phe_M_signal152.668182
Corner-Avg:10228,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal178.236328
Spike_AFFX-r2-Ec-bioB_3_signal148.250900
Spike_AFFX-r2-Bs-lys_M_signal83.658821
Spike_AFFX-r2-P1-cre_3_signal7861.561523
Spike_AFFX-r2-Bs-lys_3-5-ratio1.060054
Spike_AFFX-r2-Bs-dap_M_signal669.871216
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.688197
Spike_AFFX-r2-Ec-bioB_avg-signal154.432693
Spike_AFFX-r2-Bs-thr_avg-signal342.457886
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1988.684204
Spike_AFFX-r2-Bs-phe_5_signal204.309265
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2708.388428
RawQ2.679542
Spike_AFFX-r2-Bs-lys_5_signal77.629120
Signal(A)5.063368
%A38.395439
Signal(All)150.701828
Corner+Avg:99,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal560.305725
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal173.805298
Spike_AFFX-r2-Ec-bioD_avg-signal2348.536377
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.850941
Spike_AFFX-r2-Bs-lys_avg-signal81.193001
Spike_AFFX-r2-P1-cre_avg-signal7171.012207
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.753617
Spike_AFFX-r2-Bs-thr_3_signal533.921143
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-signal176.927567
Spike_AFFX-r2-Bs-dap_3_signal954.954346
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.361900
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal520.646423
#M400
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.291077
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.076173
Spike_AFFX-r2-Bs-thr_M_signal348.687775
Signal(P)248.029358
Spike_AFFX-r2-Bs-phe_3-5-ratio0.850697
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10541,Count:9
Spike_AFFX-r2-P1-cre_5_signal6480.462891
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8758
Signal(M)17.667757
BackgroundAvg:63.59,Std:0.72,Min:61.8,Max:65.7
Spike_AFFX-r2-Ec-bioC_avg-signal540.476074
Spike_AFFX-r2-Bs-dap_avg-signal670.031311
Spike_AFFX-r2-Bs-dap_3-5-ratio2.478672
Spike_AFFX-r2-Ec-bioB_5_signal136.810867
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.754861
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-11_Fenclorim_24hr_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 ("Skipsey_1-11_Fenclorim_24hr_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: Skipsey_1-11_Fenclorim_24hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Secondly the safener compound fenclorim was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.601172
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-ratio1.300418
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.936666
Spike_AFFX-r2-Bs-dap_5_signal274.402039
NoiseAvg:3.07,Std:0.52,Min:2.7,Max:6.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal73.161430
#P14636
Spike_AFFX-r2-Bs-phe_M_signal108.982742
Corner-Avg:13273,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal128.245575
Spike_AFFX-r2-Ec-bioB_3_signal83.664261
Spike_AFFX-r2-Bs-lys_M_signal49.650070
Spike_AFFX-r2-P1-cre_3_signal5449.053711
Spike_AFFX-r2-Bs-lys_3-5-ratio1.049242
Spike_AFFX-r2-Bs-dap_M_signal447.418793
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.484344
Spike_AFFX-r2-Ec-bioB_avg-signal100.410400
Spike_AFFX-r2-Bs-thr_avg-signal193.341965
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal999.760681
Spike_AFFX-r2-Bs-phe_5_signal124.111389
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1602.069092
RawQ2.676944
Spike_AFFX-r2-Bs-lys_5_signal61.002293
Signal(A)3.791160
%A34.230602
Signal(All)140.475433
Corner+Avg:113,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal333.519928
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal130.771545
Spike_AFFX-r2-Ec-bioD_avg-signal1300.914917
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.164841
Spike_AFFX-r2-Bs-lys_avg-signal58.219513
Spike_AFFX-r2-P1-cre_avg-signal4819.643555
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_signal328.081024
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-signal121.288551
Spike_AFFX-r2-Bs-dap_3_signal627.889954
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.602453
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal312.704559
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal64.006180
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.066566
Spike_AFFX-r2-Bs-thr_M_signal178.783417
Signal(P)216.539139
Spike_AFFX-r2-Bs-phe_3-5-ratio1.053663
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10851,Count:9
Spike_AFFX-r2-P1-cre_5_signal4190.233887
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7808
Signal(M)14.690082
BackgroundAvg:67.76,Std:0.99,Min:64.4,Max:70.4
Spike_AFFX-r2-Ec-bioC_avg-signal323.112244
Spike_AFFX-r2-Bs-dap_avg-signal449.903564
Spike_AFFX-r2-Bs-dap_3-5-ratio2.288212
Spike_AFFX-r2-Ec-bioB_5_signal89.321358
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.601172
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-12_Fenclorim_24hr_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 ("Skipsey_1-12_Fenclorim_24hr_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: Skipsey_1-12_Fenclorim_24hr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Secondly the safener compound fenclorim was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.730928
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-ratio1.281695
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.055430
Spike_AFFX-r2-Bs-dap_5_signal391.055908
NoiseAvg:2.77,Std:0.10,Min:2.5,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_signal161.934387
#P13950
Spike_AFFX-r2-Bs-phe_M_signal167.591110
Corner-Avg:12926,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.692337
Spike_AFFX-r2-Ec-bioB_3_signal79.046310
Spike_AFFX-r2-Bs-lys_M_signal76.189850
Spike_AFFX-r2-P1-cre_3_signal5096.832031
Spike_AFFX-r2-Bs-lys_3-5-ratio1.362568
Spike_AFFX-r2-Bs-dap_M_signal747.475952
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.408838
Spike_AFFX-r2-Ec-bioB_avg-signal91.211182
Spike_AFFX-r2-Bs-thr_avg-signal415.906830
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal992.594849
Spike_AFFX-r2-Bs-phe_5_signal233.233658
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1838.064209
RawQ2.708858
Spike_AFFX-r2-Bs-lys_5_signal94.649689
Signal(A)4.686287
%A36.909252
Signal(All)145.186035
Corner+Avg:114,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal284.982208
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal228.686157
Spike_AFFX-r2-Ec-bioD_avg-signal1415.329590
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.157387
Spike_AFFX-r2-Bs-lys_avg-signal99.935402
Spike_AFFX-r2-P1-cre_avg-signal4536.732910
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.933363
Spike_AFFX-r2-Bs-thr_3_signal713.942505
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-signal209.836975
Spike_AFFX-r2-Bs-dap_3_signal1017.651672
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.851777
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal316.831207
#M441
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal128.966675
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.899476
Spike_AFFX-r2-Bs-thr_M_signal371.843689
Signal(P)234.048172
Spike_AFFX-r2-Bs-phe_3-5-ratio0.980502
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9387,Count:9
Spike_AFFX-r2-P1-cre_5_signal3976.633545
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8419
Signal(M)16.479685
BackgroundAvg:65.77,Std:0.54,Min:64.4,Max:67.4
Spike_AFFX-r2-Ec-bioC_avg-signal300.906708
Spike_AFFX-r2-Bs-dap_avg-signal718.727844
Spike_AFFX-r2-Bs-dap_3-5-ratio2.602318
Spike_AFFX-r2-Ec-bioB_5_signal74.894913
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.730928
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-13_CMP_4hr_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 ("Skipsey_1-13_CMP_4hr_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: Skipsey_1-13_CMP_4hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Finally 4-chloro-6-methyl-2-phenylpyrimidine (CMP) was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.538743
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-ratio1.230958
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.126032
Spike_AFFX-r2-Bs-dap_5_signal109.531082
NoiseAvg:3.03,Std:0.11,Min:2.8,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_signal41.713360
#P14565
Spike_AFFX-r2-Bs-phe_M_signal53.714676
Corner-Avg:12514,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.977074
Spike_AFFX-r2-Ec-bioB_3_signal57.880413
Spike_AFFX-r2-Bs-lys_M_signal21.787804
Spike_AFFX-r2-P1-cre_3_signal3350.717285
Spike_AFFX-r2-Bs-lys_3-5-ratio1.634713
Spike_AFFX-r2-Bs-dap_M_signal216.208359
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.908963
Spike_AFFX-r2-Ec-bioB_avg-signal61.753201
Spike_AFFX-r2-Bs-thr_avg-signal118.343925
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal566.927307
Spike_AFFX-r2-Bs-phe_5_signal56.029030
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1026.942993
RawQ2.626196
Spike_AFFX-r2-Bs-lys_5_signal34.580368
Signal(A)4.373270
%A34.340202
Signal(All)138.414673
Corner+Avg:109,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.737427
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.237507
Spike_AFFX-r2-Ec-bioD_avg-signal796.935181
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.853573
Spike_AFFX-r2-Bs-lys_avg-signal37.632389
Spike_AFFX-r2-P1-cre_avg-signal3036.379395
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.806225
Spike_AFFX-r2-Bs-thr_3_signal204.769333
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-signal56.993732
Spike_AFFX-r2-Bs-dap_3_signal333.904266
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.811419
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal194.167191
#M412
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.528992
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.059589
Spike_AFFX-r2-Bs-thr_M_signal108.549080
Signal(P)213.989655
Spike_AFFX-r2-Bs-phe_3-5-ratio1.092960
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8689,Count:9
Spike_AFFX-r2-P1-cre_5_signal2722.041504
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7833
Signal(M)15.106203
BackgroundAvg:69.21,Std:0.49,Min:67.3,Max:70.2
Spike_AFFX-r2-Ec-bioC_avg-signal199.952301
Spike_AFFX-r2-Bs-dap_avg-signal219.881226
Spike_AFFX-r2-Bs-dap_3-5-ratio3.048489
Spike_AFFX-r2-Ec-bioB_5_signal51.402115
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.538743
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-14_CMP_4hr_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 ("Skipsey_1-14_CMP_4hr_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: Skipsey_1-14_CMP_4hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Finally 4-chloro-6-methyl-2-phenylpyrimidine (CMP) was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.699805
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-ratio1.066431
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.537691
Spike_AFFX-r2-Bs-dap_5_signal307.135986
NoiseAvg:2.69,Std:0.11,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal136.176453
#P14043
Spike_AFFX-r2-Bs-phe_M_signal126.722198
Corner-Avg:13875,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal126.623024
Spike_AFFX-r2-Ec-bioB_3_signal107.028687
Spike_AFFX-r2-Bs-lys_M_signal70.513832
Spike_AFFX-r2-P1-cre_3_signal4837.749023
Spike_AFFX-r2-Bs-lys_3-5-ratio0.934462
Spike_AFFX-r2-Bs-dap_M_signal619.395752
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.059270
Spike_AFFX-r2-Ec-bioB_avg-signal101.085060
Spike_AFFX-r2-Bs-thr_avg-signal271.511414
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1034.598145
Spike_AFFX-r2-Bs-phe_5_signal229.253464
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1513.730591
RawQ2.652689
Spike_AFFX-r2-Bs-lys_5_signal88.573181
Signal(A)4.545681
%A36.427006
Signal(All)146.038239
Corner+Avg:119,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal349.022980
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal149.737778
Spike_AFFX-r2-Ec-bioD_avg-signal1274.164307
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.565102
Spike_AFFX-r2-Bs-lys_avg-signal80.618431
Spike_AFFX-r2-P1-cre_avg-signal4687.070801
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.007891
Spike_AFFX-r2-Bs-thr_3_signal416.600494
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-signal168.571152
Spike_AFFX-r2-Bs-dap_3_signal792.842896
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.463110
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal294.071075
#M458
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.768272
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.186866
Spike_AFFX-r2-Bs-thr_M_signal261.757263
Signal(P)233.978180
Spike_AFFX-r2-Bs-phe_3-5-ratio0.653154
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10165,Count:9
Spike_AFFX-r2-P1-cre_5_signal4536.392578
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8309
Signal(M)16.608799
BackgroundAvg:78.42,Std:0.52,Min:76.6,Max:79.3
Spike_AFFX-r2-Ec-bioC_avg-signal321.547028
Spike_AFFX-r2-Bs-dap_avg-signal573.124878
Spike_AFFX-r2-Bs-dap_3-5-ratio2.581407
Spike_AFFX-r2-Ec-bioB_5_signal69.603500
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.699805
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-15_CMP_4hr_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Skipsey_1-15_CMP_4hr_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: Skipsey_1-15_CMP_4hr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 4hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Finally 4-chloro-6-methyl-2-phenylpyrimidine (CMP) was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.613156
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-ratio1.250621
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.974857
Spike_AFFX-r2-Bs-dap_5_signal148.842987
NoiseAvg:3.00,Std:0.13,Min:2.7,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal50.304577
#P14760
Spike_AFFX-r2-Bs-phe_M_signal47.127251
Corner-Avg:11219,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.159912
Spike_AFFX-r2-Ec-bioB_3_signal65.271278
Spike_AFFX-r2-Bs-lys_M_signal22.986645
Spike_AFFX-r2-P1-cre_3_signal3332.947998
Spike_AFFX-r2-Bs-lys_3-5-ratio1.556641
Spike_AFFX-r2-Bs-dap_M_signal244.990417
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.730830
Spike_AFFX-r2-Ec-bioB_avg-signal70.795296
Spike_AFFX-r2-Bs-thr_avg-signal108.271858
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal510.820465
Spike_AFFX-r2-Bs-phe_5_signal61.471478
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal871.944824
RawQ2.674414
Spike_AFFX-r2-Bs-lys_5_signal26.571146
Signal(A)4.409811
%A33.572994
Signal(All)137.340012
Corner+Avg:87,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal202.288910
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal70.974854
Spike_AFFX-r2-Ec-bioD_avg-signal691.382629
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.708458
Spike_AFFX-r2-Bs-lys_avg-signal30.306505
Spike_AFFX-r2-P1-cre_avg-signal2998.990723
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.718544
Spike_AFFX-r2-Bs-thr_3_signal137.373230
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-signal59.857861
Spike_AFFX-r2-Bs-dap_3_signal369.402466
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.706950
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal213.092239
#M392
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.361732
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.949302
Spike_AFFX-r2-Bs-thr_M_signal137.137787
Signal(P)209.529526
Spike_AFFX-r2-Bs-phe_3-5-ratio1.154598
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10337,Count:9
Spike_AFFX-r2-P1-cre_5_signal2665.033691
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7658
Signal(M)16.070774
BackgroundAvg:72.22,Std:0.38,Min:71.2,Max:73.7
Spike_AFFX-r2-Ec-bioC_avg-signal207.690582
Spike_AFFX-r2-Bs-dap_avg-signal254.411942
Spike_AFFX-r2-Bs-dap_3-5-ratio2.481827
Spike_AFFX-r2-Ec-bioB_5_signal66.954697
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.613156
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-16_CMP_24hr_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 ("Skipsey_1-16_CMP_24hr_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: Skipsey_1-16_CMP_24hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Finally 4-chloro-6-methyl-2-phenylpyrimidine (CMP) was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.637664
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-ratio1.315182
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.081064
Spike_AFFX-r2-Bs-dap_5_signal241.291473
NoiseAvg:2.94,Std:0.13,Min:2.7,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal76.783081
#P15114
Spike_AFFX-r2-Bs-phe_M_signal88.859863
Corner-Avg:14744,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal126.590874
Spike_AFFX-r2-Ec-bioB_3_signal89.406609
Spike_AFFX-r2-Bs-lys_M_signal39.292694
Spike_AFFX-r2-P1-cre_3_signal5117.933594
Spike_AFFX-r2-Bs-lys_3-5-ratio0.994691
Spike_AFFX-r2-Bs-dap_M_signal381.721924
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.627096
Spike_AFFX-r2-Ec-bioB_avg-signal99.566628
Spike_AFFX-r2-Bs-thr_avg-signal147.341873
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal977.345764
Spike_AFFX-r2-Bs-phe_5_signal128.502808
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1496.962402
RawQ2.724931
Spike_AFFX-r2-Bs-lys_5_signal47.819016
Signal(A)3.974072
%A31.994740
Signal(All)137.071182
Corner+Avg:118,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal340.313385
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal96.560623
Spike_AFFX-r2-Ec-bioD_avg-signal1237.154053
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.260414
Spike_AFFX-r2-Bs-lys_avg-signal44.892288
Spike_AFFX-r2-P1-cre_avg-signal4504.679688
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.744849
Spike_AFFX-r2-Bs-thr_3_signal201.716522
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-signal104.641090
Spike_AFFX-r2-Bs-dap_3_signal461.532898
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.531661
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal286.484772
#M398
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.565151
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.187894
Spike_AFFX-r2-Bs-thr_M_signal163.526047
Signal(P)204.587814
Spike_AFFX-r2-Bs-phe_3-5-ratio0.751428
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11612,Count:9
Spike_AFFX-r2-P1-cre_5_signal3891.425293
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7298
Signal(M)13.694677
BackgroundAvg:69.74,Std:0.45,Min:68.0,Max:70.4
Spike_AFFX-r2-Ec-bioC_avg-signal313.399078
Spike_AFFX-r2-Bs-dap_avg-signal361.515411
Spike_AFFX-r2-Bs-dap_3-5-ratio1.912761
Spike_AFFX-r2-Ec-bioB_5_signal82.702415
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.637664
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-17_CMP_24hr_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 ("Skipsey_1-17_CMP_24hr_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: Skipsey_1-17_CMP_24hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Finally 4-chloro-6-methyl-2-phenylpyrimidine (CMP) was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.447255
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-ratio1.257027
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.175726
Spike_AFFX-r2-Bs-dap_5_signal239.001205
NoiseAvg:2.99,Std:0.09,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal79.631058
#P15171
Spike_AFFX-r2-Bs-phe_M_signal83.855164
Corner-Avg:13671,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.975182
Spike_AFFX-r2-Ec-bioB_3_signal66.712128
Spike_AFFX-r2-Bs-lys_M_signal35.339771
Spike_AFFX-r2-P1-cre_3_signal4142.411621
Spike_AFFX-r2-Bs-lys_3-5-ratio1.013297
Spike_AFFX-r2-Bs-dap_M_signal423.530212
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.758310
Spike_AFFX-r2-Ec-bioB_avg-signal75.476181
Spike_AFFX-r2-Bs-thr_avg-signal173.411697
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal823.819641
Spike_AFFX-r2-Bs-phe_5_signal118.039131
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1158.452515
RawQ2.661507
Spike_AFFX-r2-Bs-lys_5_signal52.556240
Signal(A)3.217778
%A31.858833
Signal(All)134.677063
Corner+Avg:116,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal301.016296
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal107.900345
Spike_AFFX-r2-Ec-bioD_avg-signal991.136108
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.510300
Spike_AFFX-r2-Bs-lys_avg-signal47.050365
Spike_AFFX-r2-P1-cre_avg-signal3718.908203
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.630864
Spike_AFFX-r2-Bs-thr_3_signal299.278229
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-signal103.264885
Spike_AFFX-r2-Bs-dap_3_signal563.407776
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.406197
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal243.709534
#M372
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.255085
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.235144
Spike_AFFX-r2-Bs-thr_M_signal141.325821
Signal(P)200.665100
Spike_AFFX-r2-Bs-phe_3-5-ratio0.914107
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11575,Count:9
Spike_AFFX-r2-P1-cre_5_signal3295.405029
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7267
Signal(M)11.585998
BackgroundAvg:66.91,Std:0.46,Min:65.6,Max:68.0
Spike_AFFX-r2-Ec-bioC_avg-signal272.362915
Spike_AFFX-r2-Bs-dap_avg-signal408.646393
Spike_AFFX-r2-Bs-dap_3-5-ratio2.357343
Spike_AFFX-r2-Ec-bioB_5_signal56.741222
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.447255
NF1.000000
HZ4
Tau0.015000

Slide: Skipsey_1-18_CMP_24hr_Rep3_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 ("Skipsey_1-18_CMP_24hr_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: Skipsey_1-18_CMP_24hr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 24hr
Growth Conditions:
Growth conditionsWildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.
Tissue: root
in vivo Treatment:
TreatmentThe three treatments employed in this study were addition of acetone as a control treatment as this solvent carrier was used to dissolve the compounds in the other treatments. Finally 4-chloro-6-methyl-2-phenylpyrimidine (CMP) was added to cultures. Treatment compounds were added to Arabidopsis root cultures for 4 h and 24 h periods prior to RNA extraction.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.54538
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-ratio1.366017
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.359363
Spike_AFFX-r2-Bs-dap_5_signal228.770569
NoiseAvg:3.05,Std:0.09,Min:2.8,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_signal74.473373
#P15009
Spike_AFFX-r2-Bs-phe_M_signal64.935593
Corner-Avg:12687,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.005051
Spike_AFFX-r2-Ec-bioB_3_signal69.233765
Spike_AFFX-r2-Bs-lys_M_signal37.817825
Spike_AFFX-r2-P1-cre_3_signal4100.452637
Spike_AFFX-r2-Bs-lys_3-5-ratio1.100939
Spike_AFFX-r2-Bs-dap_M_signal353.063263
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.731183
Spike_AFFX-r2-Ec-bioB_avg-signal66.723274
Spike_AFFX-r2-Bs-thr_avg-signal175.191345
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal690.309021
Spike_AFFX-r2-Bs-phe_5_signal112.345764
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1116.072998
RawQ2.797201
Spike_AFFX-r2-Bs-lys_5_signal51.808178
Signal(A)4.031335
%A32.560280
Signal(All)135.037872
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal269.781189
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal121.875122
Spike_AFFX-r2-Ec-bioD_avg-signal903.191040
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.800087
Spike_AFFX-r2-Bs-lys_avg-signal48.887890
Spike_AFFX-r2-P1-cre_avg-signal3551.105957
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_signal277.873749
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-signal99.718834
Spike_AFFX-r2-Bs-dap_3_signal506.250305
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.616773
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal248.219315
#M374
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.037659
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.086866
Spike_AFFX-r2-Bs-thr_M_signal173.226898
Signal(P)202.893219
Spike_AFFX-r2-Bs-phe_3-5-ratio1.084822
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10058,Count:9
Spike_AFFX-r2-P1-cre_5_signal3001.759033
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7427
Signal(M)13.499583
BackgroundAvg:71.84,Std:0.55,Min:69.6,Max:73.1
Spike_AFFX-r2-Ec-bioC_avg-signal259.000244
Spike_AFFX-r2-Bs-dap_avg-signal362.694733
Spike_AFFX-r2-Bs-dap_3-5-ratio2.212917
Spike_AFFX-r2-Ec-bioB_5_signal50.931019
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.545380
NF1.000000
HZ4
Tau0.015000


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