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Experiment: Measurement of pre-existing and newly transcribed mRNA at two ambient temperatures

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-670

In Arabidopsis thaliana a number of genes show altered transcript abundances at different ambient temperatures. As with other biochemical reactions, mRNA transcription and decay rates might be expected to increase passively with increasing temperature but it is not clear to what degree active temperature responses play a role in temperature-regulated genome-wide gene expression changes.Using a non-perturbing base analogue (4-thiouridine) labelling and separation method we have measured the relative abundances of both labelled, newly transcribed transcripts and unlabelled, pre-existing transcripts. Together with unseparated samples and samples taken at the start of the labelling time, these arrays have been used to calculate transcription and decay rates of the Arabidopsis thaliana transcriptome at two ambient temperatures.

About the Experimenter

Name:Dr Kate Sidaway-Lee
Head of Lab Name:Dr Steven Penfield
Lab:
Address:Geoffrey Pope Building
University of Exeter
Stocker Road
Exeter
Devon
Postcode: EX4 4QD
Country: UK
 

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: growth_condition_design;
Number of Slides:24
 
Experimental Parameters:
parameter Newly transcribed
parameter Pre-existing
parameter Total
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Sidaway-Lee: Measurement of pre-existing and newly transcribed mRNA at two ambient temperatures

Slide: Sidaway-Lee_670-17_0_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Sidaway-Lee_670-17_0_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: Sidaway-Lee_670-17_0_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22 °C average, 22 °C day, 22 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.559546
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-ratio1.354287
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.971399
Spike_AFFX-r2-Bs-dap_5_signal19.116753
NoiseAvg:1.40,Std:0.05,Min:1.2,Max:1.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.865789
#P13944
Spike_AFFX-r2-Bs-phe_M_signal4.640282
Corner-Avg:1960,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal47.090225
Spike_AFFX-r2-Ec-bioB_3_signal39.825436
Spike_AFFX-r2-Bs-lys_M_signal0.234153
Spike_AFFX-r2-P1-cre_3_signal2629.991699
Spike_AFFX-r2-Bs-lys_3-5-ratio10.490237
Spike_AFFX-r2-Bs-dap_M_signal37.480782
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.299808
Spike_AFFX-r2-Ec-bioB_avg-signal42.637890
Spike_AFFX-r2-Bs-thr_avg-signal17.904535
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal527.622864
Spike_AFFX-r2-Bs-phe_5_signal2.121955
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal728.764832
RawQ1.737592
Spike_AFFX-r2-Bs-lys_5_signal2.664430
Signal(A)5.526536
%A36.970627
Signal(All)134.240143
Corner+Avg:15,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal138.455093
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal9.530973
Spike_AFFX-r2-Ec-bioD_avg-signal628.193848
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.131084
Spike_AFFX-r2-Bs-lys_avg-signal10.283028
Spike_AFFX-r2-P1-cre_avg-signal2285.983398
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.898290
Spike_AFFX-r2-Bs-thr_3_signal27.289040
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-signal5.431070
Spike_AFFX-r2-Bs-dap_3_signal70.819679
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.381223
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal114.666054
#M433
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal27.950500
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.207464
Spike_AFFX-r2-Bs-thr_M_signal14.558779
Signal(P)215.648239
Spike_AFFX-r2-Bs-phe_3-5-ratio4.491601
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1571,Count:9
Spike_AFFX-r2-P1-cre_5_signal1941.975220
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8433
Signal(M)19.430218
BackgroundAvg:49.15,Std:0.58,Min:47.6,Max:51.0
Spike_AFFX-r2-Ec-bioC_avg-signal126.560577
Spike_AFFX-r2-Bs-dap_avg-signal42.472404
Spike_AFFX-r2-Bs-dap_3-5-ratio3.704587
Spike_AFFX-r2-Ec-bioB_5_signal40.998005
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.559546
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_0_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Sidaway-Lee_670-17_0_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: Sidaway-Lee_670-17_0_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22 °C average, 22 °C day, 22 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.814165
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-ratio1.152461
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.834917
Spike_AFFX-r2-Bs-dap_5_signal10.127774
NoiseAvg:0.64,Std:0.02,Min:0.5,Max:0.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.489478
#P15019
Spike_AFFX-r2-Bs-phe_M_signal10.639390
Corner-Avg:1429,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal40.941307
Spike_AFFX-r2-Ec-bioB_3_signal23.648539
Spike_AFFX-r2-Bs-lys_M_signal4.076245
Spike_AFFX-r2-P1-cre_3_signal2398.770508
Spike_AFFX-r2-Bs-lys_3-5-ratio2.695124
Spike_AFFX-r2-Bs-dap_M_signal41.190300
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.971347
Spike_AFFX-r2-Ec-bioB_avg-signal30.971418
Spike_AFFX-r2-Bs-thr_avg-signal16.845795
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal400.736694
Spike_AFFX-r2-Bs-phe_5_signal7.727681
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal594.084778
RawQ0.687171
Spike_AFFX-r2-Bs-lys_5_signal5.656370
Signal(A)3.442196
%A32.498905
Signal(All)137.821426
Corner+Avg:11,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal101.294014
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal6.216845
Spike_AFFX-r2-Ec-bioD_avg-signal497.410736
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.843925
Spike_AFFX-r2-Bs-lys_avg-signal8.325744
Spike_AFFX-r2-P1-cre_avg-signal2240.102051
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.657168
Spike_AFFX-r2-Bs-thr_3_signal25.771967
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-signal8.194638
Spike_AFFX-r2-Bs-dap_3_signal55.658562
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.482482
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal89.585182
#M378
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.244616
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.130701
Spike_AFFX-r2-Bs-thr_M_signal18.275938
Signal(P)207.300034
Spike_AFFX-r2-Bs-phe_3-5-ratio0.804490
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1038,Count:9
Spike_AFFX-r2-P1-cre_5_signal2081.433838
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7413
Signal(M)12.567018
BackgroundAvg:26.22,Std:0.15,Min:25.9,Max:26.6
Spike_AFFX-r2-Ec-bioC_avg-signal95.439598
Spike_AFFX-r2-Bs-dap_avg-signal35.658878
Spike_AFFX-r2-Bs-dap_3-5-ratio5.495636
Spike_AFFX-r2-Ec-bioB_5_signal28.324411
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.814165
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_0_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Sidaway-Lee_670-17_0_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: Sidaway-Lee_670-17_0_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.279294
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-ratio1.167738
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.188387
Spike_AFFX-r2-Bs-dap_5_signal9.393351
NoiseAvg:1.01,Std:0.03,Min:0.9,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.708839
#P14784
Spike_AFFX-r2-Bs-phe_M_signal9.893782
Corner-Avg:1842,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal32.052689
Spike_AFFX-r2-Ec-bioB_3_signal28.289520
Spike_AFFX-r2-Bs-lys_M_signal3.580729
Spike_AFFX-r2-P1-cre_3_signal1858.804199
Spike_AFFX-r2-Bs-lys_3-5-ratio3.900776
Spike_AFFX-r2-Bs-dap_M_signal34.692516
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.818810
Spike_AFFX-r2-Ec-bioB_avg-signal28.049057
Spike_AFFX-r2-Bs-thr_avg-signal15.125572
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal396.682495
Spike_AFFX-r2-Bs-phe_5_signal6.412351
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal581.801636
RawQ1.404729
Spike_AFFX-r2-Bs-lys_5_signal3.653903
Signal(A)3.408953
%A33.717667
Signal(All)132.609344
Corner+Avg:14,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal102.121552
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal9.005438
Spike_AFFX-r2-Ec-bioD_avg-signal489.242065
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.813675
Spike_AFFX-r2-Bs-lys_avg-signal7.162564
Spike_AFFX-r2-P1-cre_avg-signal1725.301514
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal21.729750
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-signal8.437190
Spike_AFFX-r2-Bs-dap_3_signal40.727131
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.466668
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal92.833961
#M335
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal14.253059
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.100045
Spike_AFFX-r2-Bs-thr_M_signal15.938128
Signal(P)202.554016
Spike_AFFX-r2-Bs-phe_3-5-ratio1.404390
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1268,Count:9
Spike_AFFX-r2-P1-cre_5_signal1591.798950
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7691
Signal(M)12.067143
BackgroundAvg:45.53,Std:0.26,Min:45.0,Max:46.2
Spike_AFFX-r2-Ec-bioC_avg-signal97.477753
Spike_AFFX-r2-Bs-dap_avg-signal28.270998
Spike_AFFX-r2-Bs-dap_3-5-ratio4.335741
Spike_AFFX-r2-Ec-bioB_5_signal23.804964
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.279294
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2T_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Sidaway-Lee_670-17_2T_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: Sidaway-Lee_670-17_2T_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.434058
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-ratio1.331638
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.256768
Spike_AFFX-r2-Bs-dap_5_signal10.590616
NoiseAvg:1.06,Std:0.05,Min:1.0,Max:1.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal1.852306
#P14613
Spike_AFFX-r2-Bs-phe_M_signal3.503171
Corner-Avg:1874,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal57.485199
Spike_AFFX-r2-Ec-bioB_3_signal46.038410
Spike_AFFX-r2-Bs-lys_M_signal3.202751
Spike_AFFX-r2-P1-cre_3_signal3097.470459
Spike_AFFX-r2-Bs-lys_3-5-ratio3.867723
Spike_AFFX-r2-Bs-dap_M_signal54.055416
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio20.174286
Spike_AFFX-r2-Ec-bioB_avg-signal46.718658
Spike_AFFX-r2-Bs-thr_avg-signal17.168810
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal747.593811
Spike_AFFX-r2-Bs-phe_5_signal15.409353
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal950.099060
RawQ1.408923
Spike_AFFX-r2-Bs-lys_5_signal6.866805
Signal(A)3.877458
%A34.217449
Signal(All)137.744553
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal162.301208
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.927102
Spike_AFFX-r2-Ec-bioD_avg-signal848.846436
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.064011
Spike_AFFX-r2-Bs-lys_avg-signal12.209485
Spike_AFFX-r2-P1-cre_avg-signal2711.765869
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.718544
Spike_AFFX-r2-Bs-thr_3_signal37.368958
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-signal11.279876
Spike_AFFX-r2-Bs-dap_3_signal74.380074
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.270876
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal157.612244
#M392
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal26.558901
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.029750
Spike_AFFX-r2-Bs-thr_M_signal12.285163
Signal(P)212.543015
Spike_AFFX-r2-Bs-phe_3-5-ratio0.968704
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1432,Count:9
Spike_AFFX-r2-P1-cre_5_signal2326.061279
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7805
Signal(M)14.792119
BackgroundAvg:47.88,Std:0.15,Min:47.4,Max:48.2
Spike_AFFX-r2-Ec-bioC_avg-signal159.956726
Spike_AFFX-r2-Bs-dap_avg-signal46.342037
Spike_AFFX-r2-Bs-dap_3-5-ratio7.023205
Spike_AFFX-r2-Ec-bioB_5_signal36.632378
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.434058
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2T_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 ("Sidaway-Lee_670-17_2T_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: Sidaway-Lee_670-17_2T_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.40759
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-ratio1.307747
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.748815
Spike_AFFX-r2-Bs-dap_5_signal16.464014
NoiseAvg:0.62,Std:0.04,Min:0.5,Max:0.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.075525
#P14455
Spike_AFFX-r2-Bs-phe_M_signal4.848301
Corner-Avg:1388,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal45.926357
Spike_AFFX-r2-Ec-bioB_3_signal31.105076
Spike_AFFX-r2-Bs-lys_M_signal3.891337
Spike_AFFX-r2-P1-cre_3_signal2708.831543
Spike_AFFX-r2-Bs-lys_3-5-ratio3.094606
Spike_AFFX-r2-Bs-dap_M_signal40.553089
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.482220
Spike_AFFX-r2-Ec-bioB_avg-signal39.523495
Spike_AFFX-r2-Bs-thr_avg-signal15.028145
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal450.337097
Spike_AFFX-r2-Bs-phe_5_signal8.697206
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal709.331970
RawQ0.738499
Spike_AFFX-r2-Bs-lys_5_signal4.979438
Signal(A)4.737447
%A34.620781
Signal(All)139.637497
Corner+Avg:10,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal116.119644
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal8.403533
Spike_AFFX-r2-Ec-bioD_avg-signal579.834534
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P63.371330
Spike_AFFX-r2-Bs-lys_avg-signal8.093391
Spike_AFFX-r2-P1-cre_avg-signal2390.102539
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.007891
Spike_AFFX-r2-Bs-thr_3_signal16.416368
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal7.316347
Spike_AFFX-r2-Bs-dap_3_signal55.468105
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.575113
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal92.301056
#M458
Spike_AFFX-r2-Bs-lys_5_detectionM
Spike_AFFX-r2-Bs-lys_3_signal15.409400
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.258053
Spike_AFFX-r2-Bs-thr_M_signal17.592543
Signal(P)217.259293
Spike_AFFX-r2-Bs-phe_3-5-ratio0.966234
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1092,Count:9
Spike_AFFX-r2-P1-cre_5_signal2071.373535
Spike_AFFX-r2-Bs-phe_M_detectionM
#A7897
Signal(M)15.800456
BackgroundAvg:26.18,Std:0.23,Min:25.7,Max:26.8
Spike_AFFX-r2-Ec-bioC_avg-signal104.210350
Spike_AFFX-r2-Bs-dap_avg-signal37.495068
Spike_AFFX-r2-Bs-dap_3-5-ratio3.369051
Spike_AFFX-r2-Ec-bioB_5_signal41.539055
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.407590
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2T_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 ("Sidaway-Lee_670-17_2T_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: Sidaway-Lee_670-17_2T_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.075026
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-ratio1.093649
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.662239
Spike_AFFX-r2-Bs-dap_5_signal10.711907
NoiseAvg:0.92,Std:0.04,Min:0.8,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.317802
#P13974
Spike_AFFX-r2-Bs-phe_M_signal6.099832
Corner-Avg:1507,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal42.818024
Spike_AFFX-r2-Ec-bioB_3_signal23.180965
Spike_AFFX-r2-Bs-lys_M_signal4.455960
Spike_AFFX-r2-P1-cre_3_signal1903.541870
Spike_AFFX-r2-Bs-lys_3-5-ratio2.918520
Spike_AFFX-r2-Bs-dap_M_signal27.901205
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.879000
Spike_AFFX-r2-Ec-bioB_avg-signal33.667648
Spike_AFFX-r2-Bs-thr_avg-signal15.575028
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal345.112396
Spike_AFFX-r2-Bs-phe_5_signal6.370745
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal569.220520
RawQ1.268439
Spike_AFFX-r2-Bs-lys_5_signal5.173928
Signal(A)5.016604
%A36.834721
Signal(All)135.606812
Corner+Avg:11,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal109.455078
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal9.799469
Spike_AFFX-r2-Ec-bioD_avg-signal457.166443
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.262604
Spike_AFFX-r2-Bs-lys_avg-signal8.243366
Spike_AFFX-r2-P1-cre_avg-signal1822.041992
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.902674
Spike_AFFX-r2-Bs-thr_3_signal23.946955
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal7.423349
Spike_AFFX-r2-Bs-dap_3_signal40.298359
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.649377
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal103.989494
#M434
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal15.100212
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.052559
Spike_AFFX-r2-Bs-thr_M_signal14.460328
Signal(P)217.765320
Spike_AFFX-r2-Bs-phe_3-5-ratio1.538198
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1110,Count:9
Spike_AFFX-r2-P1-cre_5_signal1740.542236
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8402
Signal(M)18.408886
BackgroundAvg:46.86,Std:0.17,Min:46.4,Max:47.3
Spike_AFFX-r2-Ec-bioC_avg-signal106.722290
Spike_AFFX-r2-Bs-dap_avg-signal26.303823
Spike_AFFX-r2-Bs-dap_3-5-ratio3.762015
Spike_AFFX-r2-Ec-bioB_5_signal35.003952
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.075026
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2N_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 ("Sidaway-Lee_670-17_2N_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: Sidaway-Lee_670-17_2N_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.867496
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-ratio1.207655
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.301896
Spike_AFFX-r2-Bs-dap_5_signal21.994370
NoiseAvg:0.56,Std:0.03,Min:0.5,Max:0.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.693011
#P15050
Spike_AFFX-r2-Bs-phe_M_signal18.231489
Corner-Avg:1440,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal69.620590
Spike_AFFX-r2-Ec-bioB_3_signal65.978065
Spike_AFFX-r2-Bs-lys_M_signal6.527122
Spike_AFFX-r2-P1-cre_3_signal4520.055664
Spike_AFFX-r2-Bs-lys_3-5-ratio3.100453
Spike_AFFX-r2-Bs-dap_M_signal151.204742
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio60.798828
Spike_AFFX-r2-Ec-bioB_avg-signal62.092373
Spike_AFFX-r2-Bs-thr_avg-signal67.174110
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal844.826904
Spike_AFFX-r2-Bs-phe_5_signal18.130404
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1351.375610
RawQ0.669919
Spike_AFFX-r2-Bs-lys_5_signal15.511949
Signal(A)3.850861
%A32.639194
Signal(All)136.414047
Corner+Avg:10,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal196.291962
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.150173
Spike_AFFX-r2-Ec-bioD_avg-signal1098.101318
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.979836
Spike_AFFX-r2-Bs-lys_avg-signal23.377710
Spike_AFFX-r2-P1-cre_avg-signal4131.446289
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.380973
Spike_AFFX-r2-Bs-thr_3_signal163.731888
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.837355
Spike_AFFX-r2-Bs-dap_3_signal299.559753
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.599589
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.488083
#M315
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.094063
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.081569
Spike_AFFX-r2-Bs-thr_M_signal35.097435
Signal(P)204.552444
Spike_AFFX-r2-Bs-phe_3-5-ratio2.435146
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1038,Count:9
Spike_AFFX-r2-P1-cre_5_signal3742.837402
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7445
Signal(M)14.033605
BackgroundAvg:25.80,Std:0.27,Min:25.1,Max:26.5
Spike_AFFX-r2-Ec-bioC_avg-signal188.890015
Spike_AFFX-r2-Bs-dap_avg-signal157.586288
Spike_AFFX-r2-Bs-dap_3-5-ratio13.619838
Spike_AFFX-r2-Ec-bioB_5_signal50.678455
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.867496
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2N_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 ("Sidaway-Lee_670-17_2N_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: Sidaway-Lee_670-17_2N_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:4.364827
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-ratio1.020596
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.078028
Spike_AFFX-r2-Bs-dap_5_signal48.406296
NoiseAvg:0.54,Std:0.03,Min:0.4,Max:0.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.442468
#P14385
Spike_AFFX-r2-Bs-phe_M_signal39.376511
Corner-Avg:1336,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.615891
Spike_AFFX-r2-Ec-bioB_3_signal66.618416
Spike_AFFX-r2-Bs-lys_M_signal27.622091
Spike_AFFX-r2-P1-cre_3_signal5337.187988
Spike_AFFX-r2-Bs-lys_3-5-ratio3.549377
Spike_AFFX-r2-Bs-dap_M_signal288.512238
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio37.898983
Spike_AFFX-r2-Ec-bioB_avg-signal73.010292
Spike_AFFX-r2-Bs-thr_avg-signal161.062469
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1026.018799
Spike_AFFX-r2-Bs-phe_5_signal28.540113
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1669.483643
RawQ0.643634
Spike_AFFX-r2-Bs-lys_5_signal39.328529
Signal(A)5.374991
%A35.344147
Signal(All)137.010498
Corner+Avg:10,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.245087
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal85.016006
Spike_AFFX-r2-Ec-bioD_avg-signal1347.751221
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.064445
Spike_AFFX-r2-Bs-lys_avg-signal68.847466
Spike_AFFX-r2-P1-cre_avg-signal5283.335938
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal395.758911
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-signal50.977543
Spike_AFFX-r2-Bs-dap_3_signal552.994629
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.627147
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal232.181458
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal139.591766
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.021809
Spike_AFFX-r2-Bs-thr_M_signal76.986023
Signal(P)213.753021
Spike_AFFX-r2-Bs-phe_3-5-ratio2.978825
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:748,Count:9
Spike_AFFX-r2-P1-cre_5_signal5229.483398
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8062
Signal(M)19.391685
BackgroundAvg:24.60,Std:0.12,Min:24.3,Max:24.9
Spike_AFFX-r2-Ec-bioC_avg-signal234.713272
Spike_AFFX-r2-Bs-dap_avg-signal296.637726
Spike_AFFX-r2-Bs-dap_3-5-ratio11.424023
Spike_AFFX-r2-Ec-bioB_5_signal61.796574
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF4.364827
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2N_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 ("Sidaway-Lee_670-17_2N_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: Sidaway-Lee_670-17_2N_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.815442
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.958911
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.152320
Spike_AFFX-r2-Bs-dap_5_signal36.001961
NoiseAvg:0.94,Std:0.02,Min:0.9,Max:1.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.859325
#P14151
Spike_AFFX-r2-Bs-phe_M_signal21.239759
Corner-Avg:1780,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.309418
Spike_AFFX-r2-Ec-bioB_3_signal68.482529
Spike_AFFX-r2-Bs-lys_M_signal10.500825
Spike_AFFX-r2-P1-cre_3_signal3266.693115
Spike_AFFX-r2-Bs-lys_3-5-ratio3.752718
Spike_AFFX-r2-Bs-dap_M_signal103.890991
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.987419
Spike_AFFX-r2-Ec-bioB_avg-signal68.407356
Spike_AFFX-r2-Bs-thr_avg-signal41.912930
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal733.611755
Spike_AFFX-r2-Bs-phe_5_signal17.742704
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1108.059570
RawQ1.437368
Spike_AFFX-r2-Bs-lys_5_signal9.815984
Signal(A)5.219470
%A36.462078
Signal(All)134.137817
Corner+Avg:10,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal233.926865
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.623045
Spike_AFFX-r2-Ec-bioD_avg-signal920.835693
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.038578
Spike_AFFX-r2-Bs-lys_avg-signal19.051144
Spike_AFFX-r2-P1-cre_avg-signal3336.680664
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.499342
Spike_AFFX-r2-Bs-thr_3_signal62.315552
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.201836
Spike_AFFX-r2-Bs-dap_3_signal135.646362
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.510417
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal199.162537
#M342
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.836624
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.174553
Spike_AFFX-r2-Bs-thr_M_signal42.563904
Signal(P)212.688950
Spike_AFFX-r2-Bs-phe_3-5-ratio1.218701
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1306,Count:9
Spike_AFFX-r2-P1-cre_5_signal3406.668457
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8317
Signal(M)19.041086
BackgroundAvg:46.93,Std:0.12,Min:46.6,Max:47.2
Spike_AFFX-r2-Ec-bioC_avg-signal216.544708
Spike_AFFX-r2-Bs-dap_avg-signal91.846436
Spike_AFFX-r2-Bs-dap_3-5-ratio3.767749
Spike_AFFX-r2-Ec-bioB_5_signal59.430122
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.815442
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2P_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 ("Sidaway-Lee_670-17_2P_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: Sidaway-Lee_670-17_2P_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.788512
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-ratio1.228861
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.098002
Spike_AFFX-r2-Bs-dap_5_signal5.141966
NoiseAvg:1.03,Std:0.02,Min:1.0,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal1.080341
#P13844
Spike_AFFX-r2-Bs-phe_M_signal7.775558
Corner-Avg:1655,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal46.956139
Spike_AFFX-r2-Ec-bioB_3_signal49.164959
Spike_AFFX-r2-Bs-lys_M_signal6.486729
Spike_AFFX-r2-P1-cre_3_signal2737.435547
Spike_AFFX-r2-Bs-lys_3-5-ratio2.751042
Spike_AFFX-r2-Bs-dap_M_signal41.724274
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio32.979271
Spike_AFFX-r2-Ec-bioB_avg-signal46.965946
Spike_AFFX-r2-Bs-thr_avg-signal17.441216
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal606.339905
Spike_AFFX-r2-Bs-phe_5_signal6.330069
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal932.498413
RawQ1.360058
Spike_AFFX-r2-Bs-lys_5_signal6.661122
Signal(A)5.165972
%A37.483559
Signal(All)140.239197
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.740097
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.184667
Spike_AFFX-r2-Ec-bioD_avg-signal769.419189
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P60.692680
Spike_AFFX-r2-Bs-lys_avg-signal10.490959
Spike_AFFX-r2-P1-cre_avg-signal2482.528320
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.823761
Spike_AFFX-r2-Bs-thr_3_signal35.628864
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-signal9.430098
Spike_AFFX-r2-Bs-dap_3_signal75.850723
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.537914
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal153.347244
#M416
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal18.325026
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.035168
Spike_AFFX-r2-Bs-thr_M_signal15.614442
Signal(P)227.353836
Spike_AFFX-r2-Bs-phe_3-5-ratio2.240839
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1230,Count:9
Spike_AFFX-r2-P1-cre_5_signal2227.620850
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8550
Signal(M)17.308569
BackgroundAvg:46.84,Std:0.09,Min:46.5,Max:47.1
Spike_AFFX-r2-Ec-bioC_avg-signal156.043671
Spike_AFFX-r2-Bs-dap_avg-signal40.905655
Spike_AFFX-r2-Bs-dap_3-5-ratio14.751308
Spike_AFFX-r2-Ec-bioB_5_signal44.776749
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.788512
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2P_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 ("Sidaway-Lee_670-17_2P_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: Sidaway-Lee_670-17_2P_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.852419
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-ratio1.199690
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.166846
Spike_AFFX-r2-Bs-dap_5_signal16.294815
NoiseAvg:0.76,Std:0.03,Min:0.7,Max:0.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal4.657876
#P14272
Spike_AFFX-r2-Bs-phe_M_signal7.537112
Corner-Avg:1768,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal61.431866
Spike_AFFX-r2-Ec-bioB_3_signal43.723766
Spike_AFFX-r2-Bs-lys_M_signal5.398872
Spike_AFFX-r2-P1-cre_3_signal3016.899658
Spike_AFFX-r2-Bs-lys_3-5-ratio2.030969
Spike_AFFX-r2-Bs-dap_M_signal52.048248
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.618951
Spike_AFFX-r2-Ec-bioB_avg-signal47.542465
Spike_AFFX-r2-Bs-thr_avg-signal19.766533
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal725.560669
Spike_AFFX-r2-Bs-phe_5_signal13.988972
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal951.747253
RawQ0.915586
Spike_AFFX-r2-Bs-lys_5_signal9.998313
Signal(A)4.489163
%A35.567734
Signal(All)141.505432
Corner+Avg:16,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal148.063950
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal12.280899
Spike_AFFX-r2-Ec-bioD_avg-signal838.653931
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.569050
Spike_AFFX-r2-Bs-lys_avg-signal11.901149
Spike_AFFX-r2-P1-cre_avg-signal2765.815918
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.863218
Spike_AFFX-r2-Bs-thr_3_signal30.830257
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-signal11.268994
Spike_AFFX-r2-Bs-dap_3_signal91.674500
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.311740
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal139.770096
#M425
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal20.306261
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.059339
Spike_AFFX-r2-Bs-thr_M_signal23.811466
Signal(P)223.146164
Spike_AFFX-r2-Bs-phe_3-5-ratio0.877899
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1202,Count:9
Spike_AFFX-r2-P1-cre_5_signal2514.732422
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8113
Signal(M)15.473530
BackgroundAvg:31.57,Std:0.27,Min:30.9,Max:32.2
Spike_AFFX-r2-Ec-bioC_avg-signal143.917023
Spike_AFFX-r2-Bs-dap_avg-signal53.339188
Spike_AFFX-r2-Bs-dap_3-5-ratio5.625992
Spike_AFFX-r2-Ec-bioB_5_signal37.471764
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.852419
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-17_2P_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 ("Sidaway-Lee_670-17_2P_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: Sidaway-Lee_670-17_2P_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 17°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.578913
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-ratio1.152739
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.168071
Spike_AFFX-r2-Bs-dap_5_signal12.291977
NoiseAvg:1.00,Std:0.03,Min:0.9,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.342161
#P14290
Spike_AFFX-r2-Bs-phe_M_signal5.467723
Corner-Avg:1883,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal37.448143
Spike_AFFX-r2-Ec-bioB_3_signal37.167442
Spike_AFFX-r2-Bs-lys_M_signal3.597938
Spike_AFFX-r2-P1-cre_3_signal2242.599121
Spike_AFFX-r2-Bs-lys_3-5-ratio4.486099
Spike_AFFX-r2-Bs-dap_M_signal45.732311
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.931643
Spike_AFFX-r2-Ec-bioB_avg-signal35.478363
Spike_AFFX-r2-Bs-thr_avg-signal19.287947
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal418.487579
Spike_AFFX-r2-Bs-phe_5_signal9.731694
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal661.720642
RawQ1.432132
Spike_AFFX-r2-Bs-lys_5_signal3.283502
Signal(A)3.969617
%A35.558964
Signal(All)137.970688
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal125.542786
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal11.712899
Spike_AFFX-r2-Ec-bioD_avg-signal540.104126
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P62.647961
Spike_AFFX-r2-Bs-lys_avg-signal7.203851
Spike_AFFX-r2-P1-cre_avg-signal2094.025879
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.793073
Spike_AFFX-r2-Bs-thr_3_signal23.840652
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-signal8.970772
Spike_AFFX-r2-Bs-dap_3_signal60.461555
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.581219
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal112.078499
#M409
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal14.730113
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.120133
Spike_AFFX-r2-Bs-thr_M_signal21.681021
Signal(P)217.552994
Spike_AFFX-r2-Bs-phe_3-5-ratio1.203583
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1340,Count:9
Spike_AFFX-r2-P1-cre_5_signal1945.452881
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8111
Signal(M)14.869360
BackgroundAvg:46.15,Std:0.19,Min:45.5,Max:46.6
Spike_AFFX-r2-Ec-bioC_avg-signal118.810638
Spike_AFFX-r2-Bs-dap_avg-signal39.495281
Spike_AFFX-r2-Bs-dap_3-5-ratio4.918782
Spike_AFFX-r2-Ec-bioB_5_signal31.819500
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.578913
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_0_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 ("Sidaway-Lee_670-27_0_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: Sidaway-Lee_670-27_0_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.896886
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-ratio1.230950
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.228350
Spike_AFFX-r2-Bs-dap_5_signal27.941254
NoiseAvg:0.93,Std:0.04,Min:0.8,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.531233
#P14157
Spike_AFFX-r2-Bs-phe_M_signal23.750362
Corner-Avg:2214,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal61.277969
Spike_AFFX-r2-Ec-bioB_3_signal63.867180
Spike_AFFX-r2-Bs-lys_M_signal19.047316
Spike_AFFX-r2-P1-cre_3_signal3389.892578
Spike_AFFX-r2-Bs-lys_3-5-ratio1.360070
Spike_AFFX-r2-Bs-dap_M_signal124.718880
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio25.313684
Spike_AFFX-r2-Ec-bioB_avg-signal59.046478
Spike_AFFX-r2-Bs-thr_avg-signal88.727562
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal659.609680
Spike_AFFX-r2-Bs-phe_5_signal31.423300
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal912.042358
RawQ1.379964
Spike_AFFX-r2-Bs-lys_5_signal29.878510
Signal(A)3.733567
%A36.352478
Signal(All)135.237030
Corner+Avg:13,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal176.486374
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.303333
Spike_AFFX-r2-Ec-bioD_avg-signal785.826050
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.064884
Spike_AFFX-r2-Bs-lys_avg-signal29.854227
Spike_AFFX-r2-P1-cre_avg-signal3071.887695
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.582639
Spike_AFFX-r2-Bs-thr_3_signal215.956940
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-signal33.159000
Spike_AFFX-r2-Bs-dap_3_signal254.713013
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.382700
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal176.075562
#M361
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.636856
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.002333
Spike_AFFX-r2-Bs-thr_M_signal41.694527
Signal(P)215.357178
Spike_AFFX-r2-Bs-phe_3-5-ratio1.409888
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1541,Count:9
Spike_AFFX-r2-P1-cre_5_signal2753.883057
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8292
Signal(M)13.812780
BackgroundAvg:44.29,Std:0.31,Min:43.5,Max:45.0
Spike_AFFX-r2-Ec-bioC_avg-signal176.280975
Spike_AFFX-r2-Bs-dap_avg-signal135.791046
Spike_AFFX-r2-Bs-dap_3-5-ratio9.116019
Spike_AFFX-r2-Ec-bioB_5_signal51.994293
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.896886
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_0_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Sidaway-Lee_670-27_0_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: Sidaway-Lee_670-27_0_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.355749
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-ratio1.249749
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.921366
Spike_AFFX-r2-Bs-dap_5_signal16.710815
NoiseAvg:0.99,Std:0.03,Min:0.9,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.640624
#P13550
Spike_AFFX-r2-Bs-phe_M_signal15.105216
Corner-Avg:1374,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal51.040455
Spike_AFFX-r2-Ec-bioB_3_signal42.163021
Spike_AFFX-r2-Bs-lys_M_signal11.228801
Spike_AFFX-r2-P1-cre_3_signal2380.742920
Spike_AFFX-r2-Bs-lys_3-5-ratio1.320652
Spike_AFFX-r2-Bs-dap_M_signal42.908772
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.061815
Spike_AFFX-r2-Ec-bioB_avg-signal46.321636
Spike_AFFX-r2-Bs-thr_avg-signal20.995279
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal567.768127
Spike_AFFX-r2-Bs-phe_5_signal6.037787
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal817.775757
RawQ1.395973
Spike_AFFX-r2-Bs-lys_5_signal9.872779
Signal(A)5.507945
%A39.053047
Signal(All)135.267685
Corner+Avg:11,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal171.259613
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.520807
Spike_AFFX-r2-Ec-bioD_avg-signal692.771973
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P59.403770
Spike_AFFX-r2-Bs-lys_avg-signal11.380028
Spike_AFFX-r2-P1-cre_avg-signal2142.859863
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.543183
Spike_AFFX-r2-Bs-thr_3_signal38.675423
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-signal12.887937
Spike_AFFX-r2-Bs-dap_3_signal70.998306
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.440334
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal162.428482
#M352
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal13.038503
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.054369
Spike_AFFX-r2-Bs-thr_M_signal16.669792
Signal(P)223.566681
Spike_AFFX-r2-Bs-phe_3-5-ratio2.901859
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1075,Count:9
Spike_AFFX-r2-P1-cre_5_signal1904.977051
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8908
Signal(M)20.064346
BackgroundAvg:45.85,Std:0.30,Min:45.2,Max:46.6
Spike_AFFX-r2-Ec-bioC_avg-signal166.844055
Spike_AFFX-r2-Bs-dap_avg-signal43.539295
Spike_AFFX-r2-Bs-dap_3-5-ratio4.248644
Spike_AFFX-r2-Ec-bioB_5_signal45.761421
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.355749
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_0_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Sidaway-Lee_670-27_0_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: Sidaway-Lee_670-27_0_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.126742
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-ratio1.066204
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.120623
Spike_AFFX-r2-Bs-dap_5_signal17.295351
NoiseAvg:0.93,Std:0.02,Min:0.9,Max:1.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.395341
#P13859
Spike_AFFX-r2-Bs-phe_M_signal34.152508
Corner-Avg:1821,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal73.885277
Spike_AFFX-r2-Ec-bioB_3_signal58.299034
Spike_AFFX-r2-Bs-lys_M_signal14.975760
Spike_AFFX-r2-P1-cre_3_signal3187.106934
Spike_AFFX-r2-Bs-lys_3-5-ratio2.264782
Spike_AFFX-r2-Bs-dap_M_signal137.493515
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio61.053276
Spike_AFFX-r2-Ec-bioB_avg-signal61.402691
Spike_AFFX-r2-Bs-thr_avg-signal88.549431
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal728.128235
Spike_AFFX-r2-Bs-phe_5_signal28.135588
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal987.847595
RawQ1.268514
Spike_AFFX-r2-Bs-lys_5_signal22.335085
Signal(A)4.197255
%A37.843052
Signal(All)136.394073
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal160.808472
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal60.405605
Spike_AFFX-r2-Ec-bioD_avg-signal857.987915
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.758438
Spike_AFFX-r2-Bs-lys_avg-signal29.298311
Spike_AFFX-r2-P1-cre_avg-signal3088.158203
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.398509
Spike_AFFX-r2-Bs-thr_3_signal207.296677
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal40.897900
Spike_AFFX-r2-Bs-dap_3_signal272.258667
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.356695
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal191.321625
#M319
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.584095
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.840514
Spike_AFFX-r2-Bs-thr_M_signal54.956253
Signal(P)221.479279
Spike_AFFX-r2-Bs-phe_3-5-ratio2.146947
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1138,Count:9
Spike_AFFX-r2-P1-cre_5_signal2989.209473
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8632
Signal(M)17.043798
BackgroundAvg:45.80,Std:0.11,Min:45.5,Max:46.1
Spike_AFFX-r2-Ec-bioC_avg-signal176.065048
Spike_AFFX-r2-Bs-dap_avg-signal142.349182
Spike_AFFX-r2-Bs-dap_3-5-ratio15.741725
Spike_AFFX-r2-Ec-bioB_5_signal52.023758
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.126742
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1T_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 ("Sidaway-Lee_670-27_1T_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: Sidaway-Lee_670-27_1T_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.31968
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-ratio1.408275
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.894353
Spike_AFFX-r2-Bs-dap_5_signal23.844509
NoiseAvg:0.84,Std:0.02,Min:0.8,Max:0.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.300008
#P13786
Spike_AFFX-r2-Bs-phe_M_signal27.938534
Corner-Avg:2091,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.588928
Spike_AFFX-r2-Ec-bioB_3_signal45.707325
Spike_AFFX-r2-Bs-lys_M_signal9.923450
Spike_AFFX-r2-P1-cre_3_signal3449.850342
Spike_AFFX-r2-Bs-lys_3-5-ratio1.746280
Spike_AFFX-r2-Bs-dap_M_signal136.950851
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio19.159691
Spike_AFFX-r2-Ec-bioB_avg-signal54.800949
Spike_AFFX-r2-Bs-thr_avg-signal86.927887
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal789.872314
Spike_AFFX-r2-Bs-phe_5_signal31.872932
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal991.209778
RawQ1.136084
Spike_AFFX-r2-Bs-lys_5_signal21.204569
Signal(A)4.586519
%A38.049103
Signal(All)139.542389
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal180.090683
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal40.725662
Spike_AFFX-r2-Ec-bioD_avg-signal890.541016
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.438404
Spike_AFFX-r2-Bs-lys_avg-signal22.719042
Spike_AFFX-r2-P1-cre_avg-signal2949.774902
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal197.344971
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-signal33.512379
Spike_AFFX-r2-Bs-dap_3_signal161.908218
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.254899
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal220.444031
#M345
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.029110
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.816945
Spike_AFFX-r2-Bs-thr_M_signal53.138683
Signal(P)227.564163
Spike_AFFX-r2-Bs-phe_3-5-ratio1.277751
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1258,Count:9
Spike_AFFX-r2-P1-cre_5_signal2449.699707
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8679
Signal(M)17.263504
BackgroundAvg:42.32,Std:0.11,Min:42.0,Max:42.7
Spike_AFFX-r2-Ec-bioC_avg-signal200.267365
Spike_AFFX-r2-Bs-dap_avg-signal107.567863
Spike_AFFX-r2-Bs-dap_3-5-ratio6.790168
Spike_AFFX-r2-Ec-bioB_5_signal51.106602
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.319680
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1T_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 ("Sidaway-Lee_670-27_1T_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: Sidaway-Lee_670-27_1T_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.832444
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-ratio1.282149
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.959318
Spike_AFFX-r2-Bs-dap_5_signal19.365511
NoiseAvg:0.94,Std:0.03,Min:0.8,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.665907
#P14129
Spike_AFFX-r2-Bs-phe_M_signal10.437012
Corner-Avg:1784,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal63.013145
Spike_AFFX-r2-Ec-bioB_3_signal36.956799
Spike_AFFX-r2-Bs-lys_M_signal2.840193
Spike_AFFX-r2-P1-cre_3_signal2945.496582
Spike_AFFX-r2-Bs-lys_3-5-ratio3.085114
Spike_AFFX-r2-Bs-dap_M_signal58.240662
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.510464
Spike_AFFX-r2-Ec-bioB_avg-signal46.164654
Spike_AFFX-r2-Bs-thr_avg-signal18.772886
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal651.366028
Spike_AFFX-r2-Bs-phe_5_signal8.296535
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal783.200439
RawQ1.229663
Spike_AFFX-r2-Bs-lys_5_signal6.936707
Signal(A)4.371909
%A36.431389
Signal(All)137.243164
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal143.579269
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal4.888381
Spike_AFFX-r2-Ec-bioD_avg-signal717.283203
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.942131
Spike_AFFX-r2-Bs-lys_avg-signal10.392479
Spike_AFFX-r2-P1-cre_avg-signal2621.404053
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal31.221777
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal7.873975
Spike_AFFX-r2-Bs-dap_3_signal71.317070
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.202397
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal158.490402
#M371
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal21.400537
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.905918
Spike_AFFX-r2-Bs-thr_M_signal19.430969
Signal(P)218.585327
Spike_AFFX-r2-Bs-phe_3-5-ratio0.589208
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1187,Count:9
Spike_AFFX-r2-P1-cre_5_signal2297.311523
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8310
Signal(M)15.616880
BackgroundAvg:45.88,Std:0.18,Min:45.4,Max:46.2
Spike_AFFX-r2-Ec-bioC_avg-signal151.034836
Spike_AFFX-r2-Bs-dap_avg-signal49.641083
Spike_AFFX-r2-Bs-dap_3-5-ratio3.682685
Spike_AFFX-r2-Ec-bioB_5_signal38.524017
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.832444
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1T_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 ("Sidaway-Lee_670-27_1T_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: Sidaway-Lee_670-27_1T_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.771085
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-ratio1.242218
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.100221
Spike_AFFX-r2-Bs-dap_5_signal22.998493
NoiseAvg:0.90,Std:0.02,Min:0.8,Max:1.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.414479
#P14253
Spike_AFFX-r2-Bs-phe_M_signal31.790913
Corner-Avg:1816,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal56.928009
Spike_AFFX-r2-Ec-bioB_3_signal43.268169
Spike_AFFX-r2-Bs-lys_M_signal18.767212
Spike_AFFX-r2-P1-cre_3_signal3055.136719
Spike_AFFX-r2-Bs-lys_3-5-ratio2.036626
Spike_AFFX-r2-Bs-dap_M_signal130.681854
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.532583
Spike_AFFX-r2-Ec-bioB_avg-signal46.507656
Spike_AFFX-r2-Bs-thr_avg-signal69.376198
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal669.099731
Spike_AFFX-r2-Bs-phe_5_signal42.005039
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal862.438110
RawQ1.345031
Spike_AFFX-r2-Bs-lys_5_signal18.810759
Signal(A)3.668806
%A35.962296
Signal(All)137.703247
Corner+Avg:11,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal149.373596
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.267567
Spike_AFFX-r2-Ec-bioD_avg-signal765.768921
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.485752
Spike_AFFX-r2-Bs-lys_avg-signal25.296150
Spike_AFFX-r2-P1-cre_avg-signal2757.278564
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_signal151.349289
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal37.687840
Spike_AFFX-r2-Bs-dap_3_signal219.967957
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.288953
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal157.678375
#M354
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.310478
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.947331
Spike_AFFX-r2-Bs-thr_M_signal46.364815
Signal(P)217.908264
Spike_AFFX-r2-Bs-phe_3-5-ratio0.934830
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1269,Count:9
Spike_AFFX-r2-P1-cre_5_signal2459.420410
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8203
Signal(M)14.320554
BackgroundAvg:43.33,Std:0.13,Min:42.9,Max:43.6
Spike_AFFX-r2-Ec-bioC_avg-signal153.525986
Spike_AFFX-r2-Bs-dap_avg-signal124.549438
Spike_AFFX-r2-Bs-dap_3-5-ratio9.564451
Spike_AFFX-r2-Ec-bioB_5_signal39.326782
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.771085
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1N_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 ("Sidaway-Lee_670-27_1N_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: Sidaway-Lee_670-27_1N_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.3945
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-ratio1.235206
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.846642
Spike_AFFX-r2-Bs-dap_5_signal24.046215
NoiseAvg:0.92,Std:0.02,Min:0.8,Max:1.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.999733
#P13943
Spike_AFFX-r2-Bs-phe_M_signal40.007595
Corner-Avg:2111,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.832466
Spike_AFFX-r2-Ec-bioB_3_signal46.693848
Spike_AFFX-r2-Bs-lys_M_signal21.130011
Spike_AFFX-r2-P1-cre_3_signal3743.191406
Spike_AFFX-r2-Bs-lys_3-5-ratio1.789114
Spike_AFFX-r2-Bs-dap_M_signal188.315338
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio32.906048
Spike_AFFX-r2-Ec-bioB_avg-signal58.892715
Spike_AFFX-r2-Bs-thr_avg-signal130.829147
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal832.485535
Spike_AFFX-r2-Bs-phe_5_signal46.443241
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1248.814453
RawQ1.387227
Spike_AFFX-r2-Bs-lys_5_signal27.736019
Signal(A)4.510411
%A37.466022
Signal(All)135.447922
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal204.507095
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.121777
Spike_AFFX-r2-Ec-bioD_avg-signal1040.650024
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.126698
Spike_AFFX-r2-Bs-lys_avg-signal32.829639
Spike_AFFX-r2-P1-cre_avg-signal3386.805176
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.407277
Spike_AFFX-r2-Bs-thr_3_signal296.145630
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal46.190872
Spike_AFFX-r2-Bs-dap_3_signal350.968140
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.500103
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal223.867630
#M321
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.622894
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.913518
Spike_AFFX-r2-Bs-thr_M_signal87.342110
Signal(P)218.413422
Spike_AFFX-r2-Bs-phe_3-5-ratio1.122268
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1149,Count:9
Spike_AFFX-r2-P1-cre_5_signal3030.419189
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8546
Signal(M)17.703178
BackgroundAvg:44.33,Std:0.11,Min:44.0,Max:44.8
Spike_AFFX-r2-Ec-bioC_avg-signal214.187363
Spike_AFFX-r2-Bs-dap_avg-signal187.776550
Spike_AFFX-r2-Bs-dap_3-5-ratio14.595567
Spike_AFFX-r2-Ec-bioB_5_signal55.151829
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.394500
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1N_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 ("Sidaway-Lee_670-27_1N_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: Sidaway-Lee_670-27_1N_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.359234
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-ratio1.056841
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.359308
Spike_AFFX-r2-Bs-dap_5_signal5.222618
NoiseAvg:1.08,Std:0.04,Min:1.0,Max:1.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.244234
#P13789
Spike_AFFX-r2-Bs-phe_M_signal11.454990
Corner-Avg:1966,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.453575
Spike_AFFX-r2-Ec-bioB_3_signal55.967850
Spike_AFFX-r2-Bs-lys_M_signal1.199433
Spike_AFFX-r2-P1-cre_3_signal3505.360352
Spike_AFFX-r2-Bs-lys_3-5-ratio5.220064
Spike_AFFX-r2-Bs-dap_M_signal55.852005
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.885352
Spike_AFFX-r2-Ec-bioB_avg-signal57.198395
Spike_AFFX-r2-Bs-thr_avg-signal26.874395
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal794.082275
Spike_AFFX-r2-Bs-phe_5_signal9.553452
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1126.899292
RawQ1.762620
Spike_AFFX-r2-Bs-lys_5_signal4.205201
Signal(A)5.818189
%A37.900043
Signal(All)133.418869
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal224.153931
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal15.690031
Spike_AFFX-r2-Ec-bioD_avg-signal960.490784
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P60.451557
Spike_AFFX-r2-Bs-lys_avg-signal9.118684
Spike_AFFX-r2-P1-cre_avg-signal3411.093994
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.648400
Spike_AFFX-r2-Bs-thr_3_signal57.123337
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-signal12.232825
Spike_AFFX-r2-Bs-dap_3_signal110.559372
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.419122
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal224.919601
#M376
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal21.951420
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.996596
Spike_AFFX-r2-Bs-thr_M_signal16.255615
Signal(P)216.467834
Spike_AFFX-r2-Bs-phe_3-5-ratio1.642341
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1259,Count:9
Spike_AFFX-r2-P1-cre_5_signal3316.827637
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8645
Signal(M)21.572407
BackgroundAvg:55.15,Std:0.24,Min:54.6,Max:55.9
Spike_AFFX-r2-Ec-bioC_avg-signal224.536774
Spike_AFFX-r2-Bs-dap_avg-signal57.211330
Spike_AFFX-r2-Bs-dap_3-5-ratio21.169340
Spike_AFFX-r2-Ec-bioB_5_signal41.173767
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.359234
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1N_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 ("Sidaway-Lee_670-27_1N_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: Sidaway-Lee_670-27_1N_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:3.174612
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-ratio1.146751
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.433915
Spike_AFFX-r2-Bs-dap_5_signal6.622426
NoiseAvg:0.95,Std:0.03,Min:0.9,Max:1.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal4.932770
#P13434
Spike_AFFX-r2-Bs-phe_M_signal10.764919
Corner-Avg:1565,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.797020
Spike_AFFX-r2-Ec-bioB_3_signal71.263573
Spike_AFFX-r2-Bs-lys_M_signal11.593657
Spike_AFFX-r2-P1-cre_3_signal4259.696289
Spike_AFFX-r2-Bs-lys_3-5-ratio1.311231
Spike_AFFX-r2-Bs-dap_M_signal49.730072
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.855415
Spike_AFFX-r2-Ec-bioB_avg-signal67.919731
Spike_AFFX-r2-Bs-thr_avg-signal37.551846
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal862.717773
Spike_AFFX-r2-Bs-phe_5_signal9.106591
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1511.684570
RawQ1.432451
Spike_AFFX-r2-Bs-lys_5_signal17.736822
Signal(A)5.954342
%A39.495834
Signal(All)137.268463
Corner+Avg:10,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal230.152267
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.393902
Spike_AFFX-r2-Ec-bioD_avg-signal1187.201172
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P58.895222
Spike_AFFX-r2-Bs-lys_avg-signal17.529181
Spike_AFFX-r2-P1-cre_avg-signal3987.136719
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal78.211113
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.755136
Spike_AFFX-r2-Bs-dap_3_signal115.466263
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.752235
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal229.332947
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.257063
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.003573
Spike_AFFX-r2-Bs-thr_M_signal29.511648
Signal(P)228.472260
Spike_AFFX-r2-Bs-phe_3-5-ratio3.667003
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1311,Count:9
Spike_AFFX-r2-P1-cre_5_signal3714.577393
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9009
Signal(M)22.219751
BackgroundAvg:43.93,Std:0.19,Min:43.5,Max:44.4
Spike_AFFX-r2-Ec-bioC_avg-signal229.742615
Spike_AFFX-r2-Bs-dap_avg-signal57.272919
Spike_AFFX-r2-Bs-dap_3-5-ratio17.435644
Spike_AFFX-r2-Ec-bioB_5_signal49.698589
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF3.174612
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1P_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 ("Sidaway-Lee_670-27_1P_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: Sidaway-Lee_670-27_1P_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/17 °C average, 22/17 °C day, 22/17 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.582077
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-ratio1.168520
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.031124
Spike_AFFX-r2-Bs-dap_5_signal39.159733
NoiseAvg:0.95,Std:0.03,Min:0.8,Max:1.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.593810
#P14002
Spike_AFFX-r2-Bs-phe_M_signal49.350983
Corner-Avg:2377,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal57.614395
Spike_AFFX-r2-Ec-bioB_3_signal47.701027
Spike_AFFX-r2-Bs-lys_M_signal20.172424
Spike_AFFX-r2-P1-cre_3_signal3159.617432
Spike_AFFX-r2-Bs-lys_3-5-ratio2.175716
Spike_AFFX-r2-Bs-dap_M_signal215.203552
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio23.772955
Spike_AFFX-r2-Ec-bioB_avg-signal50.525532
Spike_AFFX-r2-Bs-thr_avg-signal105.248955
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal721.801270
Spike_AFFX-r2-Bs-phe_5_signal63.985519
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal970.820435
RawQ1.285076
Spike_AFFX-r2-Bs-lys_5_signal32.605846
Signal(A)4.043976
%A37.045155
Signal(All)141.282196
Corner+Avg:15,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal172.610352
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal95.032173
Spike_AFFX-r2-Ec-bioD_avg-signal846.310852
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.385357
Spike_AFFX-r2-Bs-lys_avg-signal41.239773
Spike_AFFX-r2-P1-cre_avg-signal2931.782471
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.569487
Spike_AFFX-r2-Bs-thr_3_signal228.073212
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-signal69.456223
Spike_AFFX-r2-Bs-dap_3_signal359.353271
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.344997
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal172.751389
#M358
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal70.941048
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.999184
Spike_AFFX-r2-Bs-thr_M_signal78.079842
Signal(P)227.355194
Spike_AFFX-r2-Bs-phe_3-5-ratio1.485214
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1838,Count:9
Spike_AFFX-r2-P1-cre_5_signal2703.947510
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8450
Signal(M)14.099721
BackgroundAvg:43.75,Std:0.11,Min:43.5,Max:44.1
Spike_AFFX-r2-Ec-bioC_avg-signal172.680878
Spike_AFFX-r2-Bs-dap_avg-signal204.572189
Spike_AFFX-r2-Bs-dap_3-5-ratio9.176601
Spike_AFFX-r2-Ec-bioB_5_signal46.261185
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.582077
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1P_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 ("Sidaway-Lee_670-27_1P_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: Sidaway-Lee_670-27_1P_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.111754
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-ratio1.389340
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.961531
Spike_AFFX-r2-Bs-dap_5_signal25.050621
NoiseAvg:1.01,Std:0.04,Min:0.9,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.051918
#P13193
Spike_AFFX-r2-Bs-phe_M_signal11.190901
Corner-Avg:1587,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal62.116394
Spike_AFFX-r2-Ec-bioB_3_signal41.934490
Spike_AFFX-r2-Bs-lys_M_signal15.924705
Spike_AFFX-r2-P1-cre_3_signal3369.761230
Spike_AFFX-r2-Bs-lys_3-5-ratio1.470640
Spike_AFFX-r2-Bs-dap_M_signal75.579926
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.543777
Spike_AFFX-r2-Ec-bioB_avg-signal49.221039
Spike_AFFX-r2-Bs-thr_avg-signal30.622559
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal774.543518
Spike_AFFX-r2-Bs-phe_5_signal8.427830
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal868.259888
RawQ1.448073
Spike_AFFX-r2-Bs-lys_5_signal12.840692
Signal(A)5.384398
%A40.166595
Signal(All)141.710083
Corner+Avg:13,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal178.212616
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.780121
Spike_AFFX-r2-Ec-bioD_avg-signal821.401733
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P57.838669
Spike_AFFX-r2-Bs-lys_avg-signal15.883144
Spike_AFFX-r2-P1-cre_avg-signal2897.600830
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.994739
Spike_AFFX-r2-Bs-thr_3_signal45.920055
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-signal11.132950
Spike_AFFX-r2-Bs-dap_3_signal83.113144
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.120996
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal182.032959
#M455
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.884037
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.979013
Spike_AFFX-r2-Bs-thr_M_signal27.895700
Signal(P)240.636612
Spike_AFFX-r2-Bs-phe_3-5-ratio1.635073
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1033,Count:9
Spike_AFFX-r2-P1-cre_5_signal2425.440430
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9162
Signal(M)18.365494
BackgroundAvg:46.08,Std:0.19,Min:45.7,Max:46.6
Spike_AFFX-r2-Ec-bioC_avg-signal180.122787
Spike_AFFX-r2-Bs-dap_avg-signal61.247894
Spike_AFFX-r2-Bs-dap_3-5-ratio3.317808
Spike_AFFX-r2-Ec-bioB_5_signal43.612225
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.111754
NF1.000000
HZ4
Tau0.015000

Slide: Sidaway-Lee_670-27_1P_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 ("Sidaway-Lee_670-27_1P_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: Sidaway-Lee_670-27_1P_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Age: 12 days
Growth Conditions:
Stratification3 days at 4°C, on MS agar.
SterilisationEthanol bleach: washed once with 100% ethanol then incubated at RT for 10mins in ethanol bleach, washed twice with 100% ethanol then left to dry in sterile hood.
ProtocolGrowth conditions were 12 hr white light (75–100 umol/msquared/s), 12 hr dark on MS agar plates, in a Sanyo MLR cabinet at 22°C. After 5 days these plants were moved to a cabinet with the same conditions except that the temperature was 27°C.
Substrate Sterilising ProcedureAutoclave
Plant SpacingN/A
Temperature22/27 °C average, 22/27 °C day, 22/27 °C night
HumidityN/A % average, N/A % day, N/A % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: The plants were removed from the plates and put into liquid MS medium the day before harvest. At the start of the timecourse, 4- thiouridine was added to the plants.
Additional Organism Information:
Sample Description
Other Information:
ecotype_habitat
Timecourse start procedureThe timecourse began 20 minutes after the lights came on

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:2.375477
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-ratio1.124087
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.868305
Spike_AFFX-r2-Bs-dap_5_signal22.541935
NoiseAvg:0.96,Std:0.03,Min:0.9,Max:1.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.833423
#P13092
Spike_AFFX-r2-Bs-phe_M_signal22.352167
Corner-Avg:1967,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.614372
Spike_AFFX-r2-Ec-bioB_3_signal48.585411
Spike_AFFX-r2-Bs-lys_M_signal15.235314
Spike_AFFX-r2-P1-cre_3_signal3720.552002
Spike_AFFX-r2-Bs-lys_3-5-ratio2.526386
Spike_AFFX-r2-Bs-dap_M_signal116.715034
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.904575
Spike_AFFX-r2-Ec-bioB_avg-signal57.384705
Spike_AFFX-r2-Bs-thr_avg-signal63.586422
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal812.858337
Spike_AFFX-r2-Bs-phe_5_signal24.676649
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1144.765015
RawQ1.331735
Spike_AFFX-r2-Bs-lys_5_signal20.855371
Signal(A)5.865874
%A40.556774
Signal(All)145.026566
Corner+Avg:12,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.731522
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.902216
Spike_AFFX-r2-Ec-bioD_avg-signal978.811646
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.395878
Spike_AFFX-r2-Bs-lys_avg-signal29.593138
Spike_AFFX-r2-P1-cre_avg-signal3515.197754
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.047348
Spike_AFFX-r2-Bs-thr_3_signal129.038452
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.310343
Spike_AFFX-r2-Bs-dap_3_signal218.726776
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.408320
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal199.048264
#M467
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal52.688725
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.033576
Spike_AFFX-r2-Bs-thr_M_signal49.887383
Signal(P)247.864670
Spike_AFFX-r2-Bs-phe_3-5-ratio1.171237
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:1428,Count:9
Spike_AFFX-r2-P1-cre_5_signal3309.843506
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9251
Signal(M)18.729362
BackgroundAvg:45.22,Std:0.22,Min:44.7,Max:45.9
Spike_AFFX-r2-Ec-bioC_avg-signal202.389893
Spike_AFFX-r2-Bs-dap_avg-signal119.327911
Spike_AFFX-r2-Bs-dap_3-5-ratio9.703106
Spike_AFFX-r2-Ec-bioB_5_signal55.954323
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.375477
NF1.000000
HZ4
Tau0.015000


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