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Experiment: Investigating the function of the circadian clock at high temperatures

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-436

A significant proportion of the Arabidopsis transcriptome is under endogenous circadian regulation, that is entrained by light-dark cycles (Reviewed in: Hall and McWatters 2005). These genes are associated with photosynthesis, metabolism, growth and photo-protection, amongst others. Hence, it is not surprising that the circadian clock has been shown as a key factor for plants fitness (Dodd et al. 2005), such that mutants which lack this endogenous control show a rather poor performance. In this experiment, we aim to investigate how important is the clock for plants growing at high temperatures, using WT (Col) and plants with no functional clock (cca1-ox line 038).

Seeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.

About the Experimenter

Name: Victor Resco
Head of Lab Name: Anhony Hall
Lab:
Address:University of Liverpool
School of Biological Sciences
Bioscience Building
Crown Street
Liverpool
Postcode: L69 7ZB
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: time_series_design; physiological_process_design
Number of Slides:8
 
Experimental Parameters:
parametertimepoint
parametertemperature
Quality Control Measures Taken:
no-plants-pooled
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Resco: Investigating the function of the circadian clock at high temperatures_genome

Slide: Resco_1-1_Col0-17ºC-1hr-before-dawn_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 ("Resco_1-1_Col0-17ºC-1hr-before-dawn_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: Resco_1-1_Col0-17ºC-1hr-before-dawn_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 1hr before dawn
Growth Conditions:
Temperature17ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.778412282467
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:
RawQ2.12
NoiseAvg:2.03,Stdev:0.04,Max:2.2,Min:1.9
Central-Avg:4991,Count:9
Corner+Avg:69,Count:32
Corner-Avg:7146,Count:32
BackgroundAvg:49.09,Stdev:0.18,Max:49.6,Min:48.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.778412282467
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Resco_1-2_Col0-17ºC-1-hr-after-dusk_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Resco_1-2_Col0-17ºC-1-hr-after-dusk_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: Resco_1-2_Col0-17ºC-1-hr-after-dusk_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 1hr after dusk
Growth Conditions:
Temperature17ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.985167860985
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:
RawQ1.99
NoiseAvg:1.98,Stdev:0.06,Max:2.2,Min:1.8
Central-Avg:4773,Count:9
Corner+Avg:62,Count:32
Corner-Avg:6410,Count:32
BackgroundAvg:49.52,Stdev:0.21,Max:50.2,Min:48.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.985167860985
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Resco_1-3_Col0-27ºC-1hr-before-dawn_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 ("Resco_1-3_Col0-27ºC-1hr-before-dawn_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: Resco_1-3_Col0-27ºC-1hr-before-dawn_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 1hr before dawn
Growth Conditions:
Temperature27ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.292783737183
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:
RawQ1.90
NoiseAvg:1.68,Stdev:0.03,Max:1.8,Min:1.6
Central-Avg:5151,Count:9
Corner+Avg:62,Count:32
Corner-Avg:6857,Count:32
BackgroundAvg:44.31,Stdev:0.16,Max:44.8,Min:43.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.292783737183
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Resco_1-4_Col0-27ºC-1-hr-after-dusk_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 ("Resco_1-4_Col0-27ºC-1-hr-after-dusk_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: Resco_1-4_Col0-27ºC-1-hr-after-dusk_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 1hr after dusk
Growth Conditions:
Temperature27ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.776735663414
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:
RawQ2.03
NoiseAvg:1.92,Stdev:0.05,Max:2.1,Min:1.8
Central-Avg:5137,Count:9
Corner+Avg:60,Count:32
Corner-Avg:6380,Count:32
BackgroundAvg:48.12,Stdev:0.35,Max:49.5,Min:47.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.776735663414
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Resco_1-5_CCA1-OX-17ºC-1hr-before-dawn_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 ("Resco_1-5_CCA1-OX-17ºC-1hr-before-dawn_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: Resco_1-5_CCA1-OX-17ºC-1hr-before-dawn_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: CCA1-ox line 038
Stock Code:
Age: 1hr before dawn
Growth Conditions:
Temperature17ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.622391879559
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:
RawQ2.22
NoiseAvg:2.35,Stdev:0.08,Max:2.5,Min:2.2
Central-Avg:6549,Count:9
Corner+Avg:80,Count:32
Corner-Avg:8180,Count:32
BackgroundAvg:56.49,Stdev:0.43,Max:57.8,Min:54.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.622391879559
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Resco_1-6_CCA1-OX-17ºC-1hr-after-dusk_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 ("Resco_1-6_CCA1-OX-17ºC-1hr-after-dusk_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: Resco_1-6_CCA1-OX-17ºC-1hr-after-dusk_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: CCA1-ox line 038
Stock Code:
Age: 1hr after dusk
Growth Conditions:
Temperature17ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.647514045238
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:
RawQ2.20
NoiseAvg:2.17,Stdev:0.05,Max:2.3,Min:2.0
Central-Avg:5280,Count:9
Corner+Avg:70,Count:32
Corner-Avg:7347,Count:32
BackgroundAvg:51.81,Stdev:0.35,Max:52.6,Min:50.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.647514045238
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Resco_1-7_CCA1-OX-27ºC-1hr-before-dawn_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 ("Resco_1-7_CCA1-OX-27ºC-1hr-before-dawn_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: Resco_1-7_CCA1-OX-27ºC-1hr-before-dawn_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: CCA1-ox line 038
Stock Code:
Age: 1hr before dawn
Growth Conditions:
Temperature27ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.77885133028
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:
RawQ1.96
NoiseAvg:1.99,Stdev:0.06,Max:2.2,Min:1.9
Central-Avg:5867,Count:9
Corner+Avg:71,Count:32
Corner-Avg:7957,Count:32
BackgroundAvg:47.74,Stdev:0.31,Max:48.4,Min:46.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.778851330280
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Resco_1-8_CCA1-OX-27ºC-1hr-after-dusk_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 ("Resco_1-8_CCA1-OX-27ºC-1hr-after-dusk_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: Resco_1-8_CCA1-OX-27ºC-1hr-after-dusk_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: CCA1-ox line 038
Stock Code:
Age: 1hr after dusk
Growth Conditions:
Temperature27ºC
Growth protocolSeeds were sown on Araflat (Arasystem, Betatech bvba, Gent, Belgium) filled with a 3:1 mixture of compost and perlite (John Innes compost No.2, KS Horticultural Products, Seaview Nurseries, Egremont, Cumbria) maintained at field capacity and containing 0.2g per l insecticide Intercept 70WS (The Scotts Company Ltd, UK), in 12L:12D cycles at 22ºC in growth chambers until two real leaves were developed (12 days) . They were then transplanted to 20 hole multicell half trays (MC20, Desch-Plantpak) containing the same soil and at the same temperature for three days to recover from the transplant stress. Finally, plants were transferred to either 12L:12D cycles (160 umolm-2s-1) and 17ºC or 27ºC. Plants, were grown for a further 7days at these two temperatures, until six to eight leaves were developed (developmental stage 1,6-1,8). At this point none of the plants had flowered.Plant material was collected one hour before dawn and one hour after dusk. A green safety light was used to harvest plants prior to dawn. We collected a composite sample of 10 plants for each treatment combination in total eight samples: 2 genotypes x 2 temperatures x 2 sample times.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.563201844692
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:
RawQ2.44
NoiseAvg:2.68,Stdev:0.30,Max:4.5,Min:2.3
Central-Avg:5835,Count:9
Corner+Avg:70,Count:32
Corner-Avg:7140,Count:32
BackgroundAvg:58.51,Stdev:0.58,Max:61.4,Min:57.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.563201844692
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015


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