NASC's International Affymetrix Service

AI logo

NASCArrays

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

Experiment: Identification of circadian transcripts that are co-regulated with [Ca2+]cyt

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-474

Our aim is to identify circadian transcripts that are co-regulated with [Ca 2+]cyt, with the eventual goal of identifying genetic regulators and targets for circadian oscillations of [Ca 2+]cyt. We have identified two conditions in which [Ca 2+]cyt behaves differently to other circadian outputs. 1. Treatment of plants with nicotinamide, a metabolic inhibitor of ADPR cyclase, abolishes the circadian oscillations of [Ca 2+]cyt however, leaf movement, CCA1, LHY, TOC1 and CAB transcript abundance and CAB promoter activity are all rhythmic albeit with a longer period (Dodd et al., 2007). 2. The toc1-1 mutant, which shortens the circadian period of all other rhythms tested, has no effect on the period of [Ca 2+]cyt oscillations (Xu et al., 2007). We will measure the circadian regulation of transcript abundance in wild type (C24), toc1-1 and nicotinamide (C24) treated plants.METHOD: Wild type (C24) and toc1-1 seeds were sown on 1/2MS 0.8% agar plates and imbibed at 4 C for 48 hours. Seedlings were grown in LD cycles of 12hL:12hD at 19 C for 11 days to entrain the oscillator. Following transfer to LL at dawn on the 12th day, 50% of the wild type seedlings were dosed with 50 mM nicotinamide every 2 hours over the entire course of the experiment. Wild type, toc1-1 and nicotinamide treated seedlings (app 100 for each sample, excluding roots) were harvested at 4 hour intervals from 49 to 93 hours in LL (12 time points covering the entire third and fourth circadian cycles.) Two independent replicates of the whole experiment will be hybridised.

About the Experimenter

Name:Dr Fiona Robertson
Head of Lab Name:Dr Alex Webb
Lab:
Address:Department of Plant Science
University of Cambridge
Downing Site
Cambridge
Postcode: CB2 3EA
Country: UK
 
Telephone Number: 01223333928

All of the data available in this website/database is free, and you are free to do whatever you please with it. If you intend to publish work based on any of this data, please acknowledge us, contact the experimenter above, and either acknowledge them or use them as co-authors in the work.

About this Experiment

Experiment Type: compound_treatment_design
Number of Slides:72
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
no-plants-pooled
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Robertson: Identification of circadian transcripts that are co-regulated with [Ca2+]cyt_genome

Slide: Robertson_1-1_WT-untreated-49hr_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 ("Robertson_1-1_WT-untreated-49hr_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: Robertson_1-1_WT-untreated-49hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.028164982796
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:
RawQ1.80
NoiseAvg:1.73,Stdev:0.05,Max:1.9,Min:1.6
Central-Avg:7494,Count:9
Corner+Avg:72,Count:32
Corner-Avg:8758,Count:32
BackgroundAvg:42.67,Stdev:0.20,Max:43.1,Min:42.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.028164982796
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-2_WT-untreated-53hr_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 ("Robertson_1-2_WT-untreated-53hr_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: Robertson_1-2_WT-untreated-53hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.608987152576
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:
RawQ2.04
NoiseAvg:2.13,Stdev:0.04,Max:2.3,Min:2.0
Central-Avg:8058,Count:9
Corner+Avg:80,Count:32
Corner-Avg:9202,Count:32
BackgroundAvg:45.86,Stdev:0.26,Max:46.3,Min:44.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.608987152576
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-3_WT-untreated-57hr_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 ("Robertson_1-3_WT-untreated-57hr_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: Robertson_1-3_WT-untreated-57hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.735542297363
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:2.13,Stdev:0.06,Max:2.4,Min:1.9
Central-Avg:6817,Count:9
Corner+Avg:74,Count:32
Corner-Avg:7855,Count:32
BackgroundAvg:48.41,Stdev:0.52,Max:49.4,Min:47.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.735542297363
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-4_WT-untreated-61hr_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 ("Robertson_1-4_WT-untreated-61hr_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: Robertson_1-4_WT-untreated-61hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.617833673954
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:
RawQ1.95
NoiseAvg:2.09,Stdev:0.06,Max:2.3,Min:1.9
Central-Avg:7900,Count:9
Corner+Avg:89,Count:32
Corner-Avg:9341,Count:32
BackgroundAvg:46.34,Stdev:0.36,Max:47.0,Min:45.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.617833673954
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-5_WT-untreated-65hr_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 ("Robertson_1-5_WT-untreated-65hr_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: Robertson_1-5_WT-untreated-65hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.9860201478
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:1.84,Stdev:0.07,Max:2.0,Min:1.7
Central-Avg:6733,Count:9
Corner+Avg:69,Count:32
Corner-Avg:7852,Count:32
BackgroundAvg:45.21,Stdev:0.30,Max:45.8,Min:44.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.986020147800
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-6_WT-untreated-69hr_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 ("Robertson_1-6_WT-untreated-69hr_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: Robertson_1-6_WT-untreated-69hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.683985173702
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:
RawQ1.93
NoiseAvg:2.04,Stdev:0.07,Max:2.3,Min:1.9
Central-Avg:7903,Count:9
Corner+Avg:84,Count:32
Corner-Avg:9068,Count:32
BackgroundAvg:46.21,Stdev:0.29,Max:46.8,Min:45.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.683985173702
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-7_WT-untreated-73hr_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 ("Robertson_1-7_WT-untreated-73hr_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: Robertson_1-7_WT-untreated-73hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.733863115311
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:
RawQ1.86
NoiseAvg:1.94,Stdev:0.07,Max:2.1,Min:1.7
Central-Avg:8705,Count:9
Corner+Avg:86,Count:32
Corner-Avg:9622,Count:32
BackgroundAvg:44.22,Stdev:0.34,Max:44.8,Min:43.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.733863115311
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-8_WT-untreated-77hr_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 ("Robertson_1-8_WT-untreated-77hr_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: Robertson_1-8_WT-untreated-77hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.639893710613
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:
RawQ2.13
NoiseAvg:2.20,Stdev:0.07,Max:2.4,Min:2.0
Central-Avg:8900,Count:9
Corner+Avg:87,Count:32
Corner-Avg:9672,Count:32
BackgroundAvg:50.56,Stdev:0.32,Max:51.1,Min:49.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.639893710613
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-9_WT-untreated-81hr_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 ("Robertson_1-9_WT-untreated-81hr_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: Robertson_1-9_WT-untreated-81hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.005141019821
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:
RawQ1.91
NoiseAvg:1.87,Stdev:0.08,Max:2.1,Min:1.7
Central-Avg:5860,Count:9
Corner+Avg:54,Count:32
Corner-Avg:6578,Count:32
BackgroundAvg:44.21,Stdev:0.24,Max:45.1,Min:43.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.005141019821
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-10_WT-untreated-85hr_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 ("Robertson_1-10_WT-untreated-85hr_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: Robertson_1-10_WT-untreated-85hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.99982714653
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:
RawQ1.79
NoiseAvg:1.65,Stdev:0.06,Max:1.9,Min:1.5
Central-Avg:6955,Count:9
Corner+Avg:62,Count:32
Corner-Avg:7895,Count:32
BackgroundAvg:41.11,Stdev:0.14,Max:41.5,Min:40.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.999827146530
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-11_WT-untreated-89hr_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 ("Robertson_1-11_WT-untreated-89hr_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: Robertson_1-11_WT-untreated-89hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.773479819298
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:
RawQ2.08
NoiseAvg:2.07,Stdev:0.08,Max:2.3,Min:1.9
Central-Avg:6254,Count:9
Corner+Avg:66,Count:32
Corner-Avg:7592,Count:32
BackgroundAvg:49.11,Stdev:0.22,Max:49.7,Min:48.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.773479819298
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-12_WT-untreated-93hr_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 ("Robertson_1-12_WT-untreated-93hr_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: Robertson_1-12_WT-untreated-93hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 12 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.03
Tissue: aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.676813781261
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:
RawQ2.18
NoiseAvg:2.22,Stdev:0.06,Max:2.4,Min:2.1
Central-Avg:7257,Count:9
Corner+Avg:74,Count:32
Corner-Avg:8389,Count:32
BackgroundAvg:51.52,Stdev:0.25,Max:52.1,Min:50.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.676813781261
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-14_Nicotinamide-treated-53hr_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 ("Robertson_1-14_Nicotinamide-treated-53hr_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: Robertson_1-14_Nicotinamide-treated-53hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.900833904743
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:
RawQ1.84
NoiseAvg:1.84,Stdev:0.06,Max:2.0,Min:1.7
Central-Avg:7274,Count:9
Corner+Avg:69,Count:32
Corner-Avg:8192,Count:32
BackgroundAvg:45.61,Stdev:0.29,Max:46.3,Min:44.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.900833904743
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-15_Nicotinamide-treated-57hr_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 ("Robertson_1-15_Nicotinamide-treated-57hr_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: Robertson_1-15_Nicotinamide-treated-57hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.004901051521
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:
RawQ1.95
NoiseAvg:1.93,Stdev:0.04,Max:2.0,Min:1.8
Central-Avg:7571,Count:9
Corner+Avg:73,Count:32
Corner-Avg:8519,Count:32
BackgroundAvg:48.09,Stdev:0.22,Max:48.7,Min:47.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.004901051521
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-16_Nicotinamide-treated-61hr_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 ("Robertson_1-16_Nicotinamide-treated-61hr_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: Robertson_1-16_Nicotinamide-treated-61hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.981855034828
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:
RawQ2.06
NoiseAvg:2.00,Stdev:0.05,Max:2.1,Min:1.9
Central-Avg:7460,Count:9
Corner+Avg:67,Count:32
Corner-Avg:8040,Count:32
BackgroundAvg:48.88,Stdev:0.23,Max:49.5,Min:48.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.981855034828
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-13_Nicotinamide-treated-49hr_Rep1_ATH1_2

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 ("Robertson_1-13_Nicotinamide-treated-49hr_Rep1_ATH1_2") 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: Robertson_1-13_Nicotinamide-treated-49hr_Rep1_ATH1_2
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.810199201107
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:
RawQ2.05
NoiseAvg:2.00,Stdev:0.07,Max:2.2,Min:1.8
Central-Avg:7277,Count:9
Corner+Avg:73,Count:32
Corner-Avg:8586,Count:32
BackgroundAvg:47.68,Stdev:0.47,Max:48.7,Min:46.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.810199201107
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-18_Nicotinamide-treated-69hr_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 ("Robertson_1-18_Nicotinamide-treated-69hr_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: Robertson_1-18_Nicotinamide-treated-69hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.743788599968
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:
RawQ2.04
NoiseAvg:2.01,Stdev:0.05,Max:2.1,Min:1.8
Central-Avg:8276,Count:9
Corner+Avg:74,Count:32
Corner-Avg:8392,Count:32
BackgroundAvg:47.35,Stdev:0.20,Max:47.7,Min:46.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.743788599968
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-19_Nicotinamide-treated-73hr_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 ("Robertson_1-19_Nicotinamide-treated-73hr_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: Robertson_1-19_Nicotinamide-treated-73hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.844463646412
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:2.14,Stdev:0.05,Max:2.3,Min:2.0
Central-Avg:8553,Count:9
Corner+Avg:80,Count:32
Corner-Avg:9133,Count:32
BackgroundAvg:49.71,Stdev:0.34,Max:50.5,Min:48.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.844463646412
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-20_Nicotinamide-treated-77hr_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 ("Robertson_1-20_Nicotinamide-treated-77hr_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: Robertson_1-20_Nicotinamide-treated-77hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.68169260025
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:
RawQ1.85
NoiseAvg:1.70,Stdev:0.04,Max:1.8,Min:1.6
Central-Avg:7784,Count:9
Corner+Avg:64,Count:32
Corner-Avg:7958,Count:32
BackgroundAvg:42.72,Stdev:0.35,Max:43.3,Min:41.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.681692600250
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-21_Nicotinamide-treated-81hr_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 ("Robertson_1-21_Nicotinamide-treated-81hr_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: Robertson_1-21_Nicotinamide-treated-81hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.29882133007
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:
RawQ1.75
NoiseAvg:1.50,Stdev:0.04,Max:1.6,Min:1.4
Central-Avg:5325,Count:9
Corner+Avg:54,Count:32
Corner-Avg:6469,Count:32
BackgroundAvg:40.97,Stdev:0.44,Max:42.2,Min:40.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.298821330070
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-22_Nicotinamide-treated-85hr_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 ("Robertson_1-22_Nicotinamide-treated-85hr_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: Robertson_1-22_Nicotinamide-treated-85hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.950332581997
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:1.95,Stdev:0.06,Max:2.1,Min:1.8
Central-Avg:7740,Count:9
Corner+Avg:67,Count:32
Corner-Avg:8237,Count:32
BackgroundAvg:45.81,Stdev:0.13,Max:46.3,Min:45.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.950332581997
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-23_Nicotinamide-treated-89hr_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 ("Robertson_1-23_Nicotinamide-treated-89hr_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: Robertson_1-23_Nicotinamide-treated-89hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.883315980434
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:
RawQ2.08
NoiseAvg:1.94,Stdev:0.05,Max:2.1,Min:1.8
Central-Avg:7661,Count:9
Corner+Avg:67,Count:32
Corner-Avg:8260,Count:32
BackgroundAvg:49.12,Stdev:0.19,Max:49.7,Min:48.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.883315980434
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-24_Nicotinamide-treated-93hr_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 ("Robertson_1-24_Nicotinamide-treated-93hr_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: Robertson_1-24_Nicotinamide-treated-93hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.757603943348
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:
RawQ2.10
NoiseAvg:2.06,Stdev:0.04,Max:2.3,Min:2.0
Central-Avg:7957,Count:9
Corner+Avg:68,Count:32
Corner-Avg:8524,Count:32
BackgroundAvg:51.54,Stdev:0.24,Max:52.1,Min:50.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.757603943348
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-25_toc1-1-49hr_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 ("Robertson_1-25_toc1-1-49hr_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: Robertson_1-25_toc1-1-49hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.935041606426
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:
RawQ1.86
NoiseAvg:1.92,Stdev:0.05,Max:2.1,Min:1.8
Central-Avg:6318,Count:9
Corner+Avg:71,Count:32
Corner-Avg:8062,Count:32
BackgroundAvg:44.13,Stdev:0.32,Max:44.8,Min:43.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.935041606426
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-26_toc1-1-53hr_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 ("Robertson_1-26_toc1-1-53hr_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: Robertson_1-26_toc1-1-53hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.189009189606
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:
RawQ1.78
NoiseAvg:1.61,Stdev:0.04,Max:1.8,Min:1.5
Central-Avg:6129,Count:9
Corner+Avg:65,Count:32
Corner-Avg:7677,Count:32
BackgroundAvg:41.35,Stdev:0.22,Max:42.2,Min:40.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.189009189606
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-27_toc1-1-57hr_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 ("Robertson_1-27_toc1-1-57hr_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: Robertson_1-27_toc1-1-57hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.702936351299
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:
RawQ2.41
NoiseAvg:2.49,Stdev:0.06,Max:2.7,Min:2.3
Central-Avg:5720,Count:9
Corner+Avg:70,Count:32
Corner-Avg:6931,Count:32
BackgroundAvg:58.93,Stdev:0.28,Max:59.4,Min:57.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.702936351299
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-28_toc1-1-61hr_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 ("Robertson_1-28_toc1-1-61hr_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: Robertson_1-28_toc1-1-61hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.571750760078
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:
RawQ1.67
NoiseAvg:1.56,Stdev:0.06,Max:1.7,Min:1.4
Central-Avg:5884,Count:9
Corner+Avg:57,Count:32
Corner-Avg:6678,Count:32
BackgroundAvg:41.94,Stdev:0.21,Max:42.4,Min:41.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.571750760078
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-29_toc1-1-65hr_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 ("Robertson_1-29_toc1-1-65hr_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: Robertson_1-29_toc1-1-65hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.759089767933
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:2.05,Stdev:0.06,Max:2.2,Min:1.8
Central-Avg:6378,Count:9
Corner+Avg:72,Count:32
Corner-Avg:7677,Count:32
BackgroundAvg:49.42,Stdev:0.41,Max:50.1,Min:47.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.759089767933
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-30_toc1-1-69hr_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 ("Robertson_1-30_toc1-1-69hr_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: Robertson_1-30_toc1-1-69hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.755473077297
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:
RawQ2.04
NoiseAvg:2.11,Stdev:0.06,Max:2.3,Min:1.9
Central-Avg:7692,Count:9
Corner+Avg:79,Count:32
Corner-Avg:8984,Count:32
BackgroundAvg:49.85,Stdev:0.41,Max:50.6,Min:48.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.755473077297
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-31_toc1-1-73hr_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 ("Robertson_1-31_toc1-1-73hr_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: Robertson_1-31_toc1-1-73hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.849183142185
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:
RawQ1.93
NoiseAvg:1.89,Stdev:0.07,Max:2.1,Min:1.8
Central-Avg:8365,Count:9
Corner+Avg:81,Count:32
Corner-Avg:9290,Count:32
BackgroundAvg:44.56,Stdev:0.37,Max:45.3,Min:43.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.849183142185
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-32_toc1-1-77hr_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 ("Robertson_1-32_toc1-1-77hr_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: Robertson_1-32_toc1-1-77hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.57197111845
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:
RawQ2.52
NoiseAvg:2.79,Stdev:0.05,Max:3.0,Min:2.7
Central-Avg:6803,Count:9
Corner+Avg:81,Count:32
Corner-Avg:7955,Count:32
BackgroundAvg:64.63,Stdev:0.40,Max:65.5,Min:63.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.571971118450
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-33_toc1-1-81hr_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 ("Robertson_1-33_toc1-1-81hr_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: Robertson_1-33_toc1-1-81hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.728355884552
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:2.24,Stdev:0.09,Max:2.6,Min:2.0
Central-Avg:7490,Count:9
Corner+Avg:70,Count:32
Corner-Avg:8121,Count:32
BackgroundAvg:51.94,Stdev:0.45,Max:53.2,Min:50.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.728355884552
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-34_toc1-1-85hr_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 ("Robertson_1-34_toc1-1-85hr_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: Robertson_1-34_toc1-1-85hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.957993149757
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:
RawQ2.04
NoiseAvg:2.02,Stdev:0.07,Max:2.2,Min:1.9
Central-Avg:6674,Count:9
Corner+Avg:68,Count:32
Corner-Avg:7591,Count:32
BackgroundAvg:50.14,Stdev:0.21,Max:50.6,Min:49.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.957993149757
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-35_toc1-1-89hr_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 ("Robertson_1-35_toc1-1-89hr_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: Robertson_1-35_toc1-1-89hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:1.045917749405
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:
RawQ1.73
NoiseAvg:1.68,Stdev:0.06,Max:1.9,Min:1.5
Central-Avg:7456,Count:9
Corner+Avg:65,Count:32
Corner-Avg:8437,Count:32
BackgroundAvg:42.60,Stdev:0.13,Max:43.0,Min:42.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.045917749405
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-36_toc1-1-93hr_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 ("Robertson_1-36_toc1-1-93hr_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: Robertson_1-36_toc1-1-93hr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.755703449249
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:
RawQ2.17
NoiseAvg:2.25,Stdev:0.06,Max:2.4,Min:2.0
Central-Avg:6861,Count:9
Corner+Avg:67,Count:32
Corner-Avg:7548,Count:32
BackgroundAvg:53.49,Stdev:0.22,Max:54.3,Min:52.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.755703449249
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-17_Nicotinamide-treated-65hr_Rep1_ATH1_2

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 ("Robertson_1-17_Nicotinamide-treated-65hr_Rep1_ATH1_2") 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: Robertson_1-17_Nicotinamide-treated-65hr_Rep1_ATH1_2
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Plant Spacing10-20 seeds clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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:0.838806331158
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:
RawQ2.10
NoiseAvg:2.04,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:7454,Count:9
Corner+Avg:68,Count:32
Corner-Avg:8322,Count:32
BackgroundAvg:50.51,Stdev:0.38,Max:51.2,Min:49.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.838806331158
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-54_Nicotinamide-treated-69hr_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 ("Robertson_1-54_Nicotinamide-treated-69hr_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: Robertson_1-54_Nicotinamide-treated-69hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.877389132977
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:2.02,Stdev:0.07,Max:2.2,Min:1.9
Central-Avg:7679,Count:9
Corner+Avg:74,Count:32
Corner-Avg:8575,Count:32
BackgroundAvg:48.60,Stdev:0.23,Max:49.1,Min:47.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.877389132977
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-53_Nicotinamide-treated-65hr_Rep2_ATH1_2

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 ("Robertson_1-53_Nicotinamide-treated-65hr_Rep2_ATH1_2") 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: Robertson_1-53_Nicotinamide-treated-65hr_Rep2_ATH1_2
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.770337224007
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:2.08,Stdev:0.08,Max:2.2,Min:1.8
Central-Avg:7423,Count:9
Corner+Avg:79,Count:32
Corner-Avg:8701,Count:32
BackgroundAvg:50.60,Stdev:0.38,Max:51.4,Min:49.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.770337224007
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-52_Nicotinamide-treated-61hr_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 ("Robertson_1-52_Nicotinamide-treated-61hr_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: Robertson_1-52_Nicotinamide-treated-61hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.352651000023
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:
RawQ1.93
NoiseAvg:1.77,Stdev:0.06,Max:2.0,Min:1.6
Central-Avg:5931,Count:9
Corner+Avg:58,Count:32
Corner-Avg:6494,Count:32
BackgroundAvg:46.04,Stdev:0.39,Max:46.9,Min:45.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.352651000023
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-51_Nicotinamide-treated-57hr_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 ("Robertson_1-51_Nicotinamide-treated-57hr_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: Robertson_1-51_Nicotinamide-treated-57hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.052229523659
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:
RawQ1.78
NoiseAvg:1.67,Stdev:0.03,Max:1.8,Min:1.6
Central-Avg:5722,Count:9
Corner+Avg:69,Count:32
Corner-Avg:7538,Count:32
BackgroundAvg:41.78,Stdev:0.28,Max:42.6,Min:41.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.052229523659
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-50_Nicotinamide-treated-53hr_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 ("Robertson_1-50_Nicotinamide-treated-53hr_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: Robertson_1-50_Nicotinamide-treated-53hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.237017035484
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:
RawQ1.84
NoiseAvg:1.67,Stdev:0.05,Max:1.8,Min:1.5
Central-Avg:6036,Count:9
Corner+Avg:69,Count:32
Corner-Avg:7863,Count:32
BackgroundAvg:42.61,Stdev:0.62,Max:44.2,Min:41.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.237017035484
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-49_Nicotinamide-treated-49hr_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 ("Robertson_1-49_Nicotinamide-treated-49hr_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: Robertson_1-49_Nicotinamide-treated-49hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.826668560505
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:
RawQ2.21
NoiseAvg:2.11,Stdev:0.06,Max:2.3,Min:1.9
Central-Avg:6180,Count:9
Corner+Avg:75,Count:32
Corner-Avg:7968,Count:32
BackgroundAvg:51.13,Stdev:0.19,Max:51.6,Min:50.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.826668560505
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-48_WT-untreated-93hr_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 ("Robertson_1-48_WT-untreated-93hr_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: Robertson_1-48_WT-untreated-93hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.196528315544
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:
RawQ1.64
NoiseAvg:1.49,Stdev:0.03,Max:1.6,Min:1.4
Central-Avg:6592,Count:9
Corner+Avg:66,Count:32
Corner-Avg:8223,Count:32
BackgroundAvg:39.35,Stdev:0.18,Max:39.9,Min:39.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.196528315544
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-47_WT-untreated-89hr_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 ("Robertson_1-47_WT-untreated-89hr_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: Robertson_1-47_WT-untreated-89hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.899015724659
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:
RawQ1.79
NoiseAvg:1.82,Stdev:0.05,Max:2.0,Min:1.7
Central-Avg:7015,Count:9
Corner+Avg:74,Count:32
Corner-Avg:8333,Count:32
BackgroundAvg:44.77,Stdev:0.21,Max:45.2,Min:44.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.899015724659
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-46_WT-untreated-85hr_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 ("Robertson_1-46_WT-untreated-85hr_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: Robertson_1-46_WT-untreated-85hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:2.442721128464
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:
RawQ1.43
NoiseAvg:1.19,Stdev:0.03,Max:1.3,Min:1.1
Central-Avg:6524,Count:9
Corner+Avg:60,Count:32
Corner-Avg:8014,Count:32
BackgroundAvg:36.03,Stdev:0.10,Max:36.4,Min:35.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF2.442721128464
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-45_WT-untreated-81hr_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 ("Robertson_1-45_WT-untreated-81hr_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: Robertson_1-45_WT-untreated-81hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.709058701992
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:
RawQ2.50
NoiseAvg:2.61,Stdev:0.06,Max:2.8,Min:2.5
Central-Avg:7282,Count:9
Corner+Avg:80,Count:32
Corner-Avg:8557,Count:32
BackgroundAvg:60.92,Stdev:0.28,Max:61.4,Min:59.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.709058701992
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-44_WT-untreated-77hr_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 ("Robertson_1-44_WT-untreated-77hr_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: Robertson_1-44_WT-untreated-77hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.010694503784
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:
RawQ1.67
NoiseAvg:1.61,Stdev:0.06,Max:1.8,Min:1.5
Central-Avg:8954,Count:9
Corner+Avg:82,Count:32
Corner-Avg:9874,Count:32
BackgroundAvg:41.26,Stdev:0.30,Max:41.9,Min:40.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.010694503784
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-43_WT-untreated-73hr_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 ("Robertson_1-43_WT-untreated-73hr_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: Robertson_1-43_WT-untreated-73hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.350565075874
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:
RawQ2.04
NoiseAvg:2.00,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:7314,Count:9
Corner+Avg:61,Count:32
Corner-Avg:7537,Count:32
BackgroundAvg:49.06,Stdev:0.50,Max:50.0,Min:47.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.350565075874
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-42_WT-untreated-69hr_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 ("Robertson_1-42_WT-untreated-69hr_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: Robertson_1-42_WT-untreated-69hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.922632694244
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:
RawQ2.37
NoiseAvg:2.52,Stdev:0.06,Max:2.7,Min:2.3
Central-Avg:6814,Count:9
Corner+Avg:63,Count:32
Corner-Avg:6741,Count:32
BackgroundAvg:58.20,Stdev:0.70,Max:59.6,Min:56.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.922632694244
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-41_WT-untreated-65hr_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 ("Robertson_1-41_WT-untreated-65hr_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: Robertson_1-41_WT-untreated-65hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.752411365509
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:
RawQ1.97
NoiseAvg:2.01,Stdev:0.05,Max:2.1,Min:1.9
Central-Avg:8152,Count:9
Corner+Avg:82,Count:32
Corner-Avg:9179,Count:32
BackgroundAvg:47.91,Stdev:0.24,Max:48.5,Min:47.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.752411365509
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-40_WT-untreated-61hr_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 ("Robertson_1-40_WT-untreated-61hr_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: Robertson_1-40_WT-untreated-61hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.183162331581
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:
RawQ1.77
NoiseAvg:1.62,Stdev:0.05,Max:1.8,Min:1.5
Central-Avg:7248,Count:9
Corner+Avg:71,Count:32
Corner-Avg:8797,Count:32
BackgroundAvg:42.28,Stdev:0.34,Max:42.9,Min:41.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.183162331581
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-39_WT-untreated-57hr_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 ("Robertson_1-39_WT-untreated-57hr_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: Robertson_1-39_WT-untreated-57hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.793272078037
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:
RawQ2.00
NoiseAvg:2.06,Stdev:0.06,Max:2.3,Min:1.9
Central-Avg:7543,Count:9
Corner+Avg:79,Count:32
Corner-Avg:9021,Count:32
BackgroundAvg:50.09,Stdev:0.25,Max:50.6,Min:49.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.793272078037
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-38_WT-untreated-53hr_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 ("Robertson_1-38_WT-untreated-53hr_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: Robertson_1-38_WT-untreated-53hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.181582212448
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:
RawQ1.88
NoiseAvg:1.73,Stdev:0.05,Max:1.8,Min:1.6
Central-Avg:6641,Count:9
Corner+Avg:65,Count:32
Corner-Avg:8041,Count:32
BackgroundAvg:43.17,Stdev:0.17,Max:43.5,Min:42.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.181582212448
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-37_WT-untreated-49hr_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 ("Robertson_1-37_WT-untreated-49hr_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: Robertson_1-37_WT-untreated-49hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.604326725006
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:2.70,Stdev:0.11,Max:3.3,Min:2.5
Central-Avg:8286,Count:9
Corner+Avg:91,Count:32
Corner-Avg:9718,Count:32
BackgroundAvg:60.38,Stdev:0.38,Max:61.5,Min:59.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.604326725006
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-55_Nicotinamide-treated-73hr_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 ("Robertson_1-55_Nicotinamide-treated-73hr_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: Robertson_1-55_Nicotinamide-treated-73hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.862892925739
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:
RawQ1.93
NoiseAvg:2.06,Stdev:0.06,Max:2.3,Min:1.9
Central-Avg:8415,Count:9
Corner+Avg:83,Count:32
Corner-Avg:9720,Count:32
BackgroundAvg:48.23,Stdev:0.22,Max:48.8,Min:47.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.862892925739
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-56_Nicotinamide-treated-77hr_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 ("Robertson_1-56_Nicotinamide-treated-77hr_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: Robertson_1-56_Nicotinamide-treated-77hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.991948127747
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:
RawQ2.30
NoiseAvg:2.33,Stdev:0.06,Max:2.5,Min:2.2
Central-Avg:8148,Count:9
Corner+Avg:77,Count:32
Corner-Avg:9345,Count:32
BackgroundAvg:55.17,Stdev:0.26,Max:55.5,Min:54.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.991948127747
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-57_Nicotinamide-treated-81hr_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 ("Robertson_1-57_Nicotinamide-treated-81hr_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: Robertson_1-57_Nicotinamide-treated-81hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.98653370142
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:1.83,Stdev:0.07,Max:2.0,Min:1.6
Central-Avg:6061,Count:9
Corner+Avg:62,Count:32
Corner-Avg:7479,Count:32
BackgroundAvg:45.39,Stdev:0.38,Max:46.3,Min:44.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.986533701420
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-58_Nicotinamide-treated-85hr_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 ("Robertson_1-58_Nicotinamide-treated-85hr_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: Robertson_1-58_Nicotinamide-treated-85hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.316752076149
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:
RawQ2.09
NoiseAvg:1.92,Stdev:0.07,Max:2.1,Min:1.7
Central-Avg:5949,Count:9
Corner+Avg:62,Count:32
Corner-Avg:7274,Count:32
BackgroundAvg:49.29,Stdev:0.81,Max:52.7,Min:47.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.316752076149
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-59_Nicotinamide-treated-89hr_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 ("Robertson_1-59_Nicotinamide-treated-89hr_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: Robertson_1-59_Nicotinamide-treated-89hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.134230017662
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:
RawQ2.19
NoiseAvg:2.02,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:6189,Count:9
Corner+Avg:62,Count:32
Corner-Avg:6923,Count:32
BackgroundAvg:52.80,Stdev:0.35,Max:53.4,Min:51.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.134230017662
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-60_Nicotinamide-treated-93hr_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 ("Robertson_1-60_Nicotinamide-treated-93hr_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: Robertson_1-60_Nicotinamide-treated-93hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Tissue: seedlings, aerial tissue
in vivo Treatment: Seedlings were dosed with 50 mM Nicotinamide every two hours from the time at which they were transferred to constant light conditions on the 12th day of growth.
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 100 seedlings.
Other Information:
ecotype_habitatC24 seed expressing CAB2:LUC were obtained from Andrew Millar, Edinburgh University. Plants were subsequently transformed with pJAAAEQ and express aequorin under the control of the the CaMV 35S promoter (Xu et al., 2007).
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.795980632305
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:
RawQ1.93
NoiseAvg:2.02,Stdev:0.08,Max:2.3,Min:1.8
Central-Avg:6875,Count:9
Corner+Avg:78,Count:32
Corner-Avg:8355,Count:32
BackgroundAvg:46.81,Stdev:0.95,Max:49.9,Min:45.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.795980632305
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-61_toc1-1-49hr_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 ("Robertson_1-61_toc1-1-49hr_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: Robertson_1-61_toc1-1-49hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.965937495232
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:
RawQ2.32
NoiseAvg:2.32,Stdev:0.05,Max:2.5,Min:2.2
Central-Avg:5625,Count:9
Corner+Avg:75,Count:32
Corner-Avg:7885,Count:32
BackgroundAvg:53.67,Stdev:0.76,Max:55.3,Min:52.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.965937495232
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-62_toc1-1-53hr_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 ("Robertson_1-62_toc1-1-53hr_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: Robertson_1-62_toc1-1-53hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.92117869854
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:
RawQ2.26
NoiseAvg:2.34,Stdev:0.06,Max:2.5,Min:2.2
Central-Avg:6283,Count:9
Corner+Avg:76,Count:32
Corner-Avg:7707,Count:32
BackgroundAvg:53.65,Stdev:0.40,Max:55.2,Min:53.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.921178698540
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-63_toc1-1-57hr_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 ("Robertson_1-63_toc1-1-57hr_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: Robertson_1-63_toc1-1-57hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.944957196712
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:
RawQ2.42
NoiseAvg:2.41,Stdev:0.06,Max:2.6,Min:2.3
Central-Avg:6738,Count:9
Corner+Avg:66,Count:32
Corner-Avg:7129,Count:32
BackgroundAvg:58.20,Stdev:0.64,Max:59.9,Min:56.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.944957196712
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-64_toc1-1-61hr_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 ("Robertson_1-64_toc1-1-61hr_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: Robertson_1-64_toc1-1-61hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.077244520187
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:
RawQ2.40
NoiseAvg:2.37,Stdev:0.05,Max:2.6,Min:2.2
Central-Avg:7508,Count:9
Corner+Avg:66,Count:32
Corner-Avg:7730,Count:32
BackgroundAvg:56.50,Stdev:0.38,Max:57.2,Min:55.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.077244520187
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-65_toc1-1-65hr_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 ("Robertson_1-65_toc1-1-65hr_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: Robertson_1-65_toc1-1-65hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.974463284016
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:
RawQ2.43
NoiseAvg:2.64,Stdev:0.08,Max:2.9,Min:2.4
Central-Avg:7214,Count:9
Corner+Avg:70,Count:32
Corner-Avg:8119,Count:32
BackgroundAvg:61.78,Stdev:0.51,Max:63.7,Min:60.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.974463284016
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-66_toc1-1-69hr_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 ("Robertson_1-66_toc1-1-69hr_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: Robertson_1-66_toc1-1-69hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.808134675026
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:
RawQ2.18
NoiseAvg:2.34,Stdev:0.03,Max:2.4,Min:2.3
Central-Avg:7255,Count:9
Corner+Avg:71,Count:32
Corner-Avg:8392,Count:32
BackgroundAvg:54.90,Stdev:0.29,Max:55.4,Min:54.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.808134675026
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-67_toc1-1-73hr_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 ("Robertson_1-67_toc1-1-73hr_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: Robertson_1-67_toc1-1-73hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.862347245216
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:
RawQ2.26
NoiseAvg:2.35,Stdev:0.04,Max:2.5,Min:2.2
Central-Avg:8371,Count:9
Corner+Avg:82,Count:32
Corner-Avg:9060,Count:32
BackgroundAvg:54.40,Stdev:0.34,Max:55.1,Min:53.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.862347245216
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-68_toc1-1-77hr_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 ("Robertson_1-68_toc1-1-77hr_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: Robertson_1-68_toc1-1-77hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.297163128853
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:
RawQ2.56
NoiseAvg:2.54,Stdev:0.08,Max:2.7,Min:2.3
Central-Avg:6694,Count:9
Corner+Avg:68,Count:32
Corner-Avg:6873,Count:32
BackgroundAvg:65.48,Stdev:0.56,Max:67.3,Min:64.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.297163128853
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-69_toc1-1-81hr_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 ("Robertson_1-69_toc1-1-81hr_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: Robertson_1-69_toc1-1-81hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.994814395905
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:
RawQ2.18
NoiseAvg:2.10,Stdev:0.05,Max:2.2,Min:2.0
Central-Avg:7459,Count:9
Corner+Avg:71,Count:32
Corner-Avg:8451,Count:32
BackgroundAvg:50.54,Stdev:0.59,Max:51.8,Min:49.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.994814395905
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-70_toc1-1-85hr_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 ("Robertson_1-70_toc1-1-85hr_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: Robertson_1-70_toc1-1-85hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.33696615696
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:
RawQ2.07
NoiseAvg:1.90,Stdev:0.05,Max:2.1,Min:1.8
Central-Avg:6176,Count:9
Corner+Avg:64,Count:32
Corner-Avg:7215,Count:32
BackgroundAvg:48.38,Stdev:0.28,Max:48.9,Min:47.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.336966156960
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-71_toc1-1-89hr_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 ("Robertson_1-71_toc1-1-89hr_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: Robertson_1-71_toc1-1-89hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:1.058370351791
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:
RawQ2.07
NoiseAvg:1.98,Stdev:0.04,Max:2.1,Min:1.9
Central-Avg:6792,Count:9
Corner+Avg:66,Count:32
Corner-Avg:7660,Count:32
BackgroundAvg:48.77,Stdev:0.36,Max:49.6,Min:47.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.058370351791
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Robertson_1-72_toc1-1_93hr_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 ("Robertson_1-72_toc1-1_93hr_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: Robertson_1-72_toc1-1_93hr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: toc1-1
Stock Code:
Age: 14 days old
Growth Conditions:
StratificationThe seeds were stratified at 4°C for 48 hours in darkness.
SterilisationSeeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.
Other Seed Preparation150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.
ProtocolSeedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19°C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.
Substrate Sterilising Procedureautoclaved
Plant Spacing20 seedlings clumped together
Temperature19 °C average, 19 °C day, 19 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Sanyo. Intensity: 70-100µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: EMS induced mutation mutation in At5g61380
Tissue: seedlings, aerial tissue
Additional Organism Information:
Sample DescriptionTotal aerial tissue (no roots) was collected for approximately 200 seedlings.
Other Information:
Timecourse start procedureThe start of the time course is the time at which the seedlings were transferred to constant light conditions.

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: 2008-11-26

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:0.867600619793
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:
RawQ2.14
NoiseAvg:2.12,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:6810,Count:9
Corner+Avg:67,Count:32
Corner-Avg:7379,Count:32
BackgroundAvg:52.50,Stdev:0.29,Max:53.1,Min:51.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.867600619793
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015


Problems? Comments? Suggestions? Contact the Affymetrix Team