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: DUO1 ectopic expression

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-439

The experiment is designed to examine changes in gene expression upon ectopic expression of the germ line transcription factor DUO1 in Arabidopsis. Plants were transformed with the vector pMDC7DUO1, allowing induction of DUO1 by treatment with estradiol. T2 seedlings were selected on agar plates containing hygromycin for 12 days before seedlings were transferred to plates containing either 2 µM 17ß-estradiol (induced), or control plates containing DMSO (non-induced). Plants were grown for 6, 12 or 24 hours before harvesting. RNA was extracted using the RNAeasy kit from Qiagen. Each sample consists of 20 seedlings combined and all treatments have been conducted in triplicate.

About the Experimenter

Name:Dr Lynette Brownfield
Head of Lab Name:Prof Twell David
Lab:
Address:Department of Biology
University of Leicester
University Rd
Leicester
Postcode: LE1 7RH
Country: UK
 
Telephone Number: 01162522266
Fax Number: 01162523330

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

Slides in this Experiment

Hybridisation Set: Brownfield: DUO1 ectopic expression_genome

Slide: Brownfield_1-1_6hr-not-induced_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 ("Brownfield_1-1_6hr-not-induced_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: Brownfield_1-1_6hr-not-induced_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 6h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2ul in 100ml) and incubated under constant light at 22°C further 6 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm
Other Information:
AlleleAt3g60460

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:0.843171715736
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:
RawQ2.36
NoiseAvg:2.37,Stdev:0.06,Max:2.6,Min:2.2
Central-Avg:5054,Count:9
Corner+Avg:65,Count:32
Corner-Avg:6184,Count:32
BackgroundAvg:57.49,Stdev:0.38,Max:58.7,Min:56.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.843171715736
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-2_6hr-not-induced_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 ("Brownfield_1-2_6hr-not-induced_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: Brownfield_1-2_6hr-not-induced_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 6h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2ul in 100ml) and incubated under constant light at 22°C further 6 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm
Other Information:
AlleleAt3g60460

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:0.849119842052
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:2.30,Stdev:0.15,Max:3.1,Min:2.1
Central-Avg:4602,Count:9
Corner+Avg:59,Count:32
Corner-Avg:6223,Count:32
BackgroundAvg:53.69,Stdev:0.39,Max:54.9,Min:52.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.849119842052
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-3_6hr-not-induced_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Brownfield_1-3_6hr-not-induced_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Brownfield_1-3_6hr-not-induced_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 6h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2ul in 100ml) and incubated under constant light at 22°C further 6 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm
Other Information:
AlleleAt3g60460

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:0.821070373058
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:
RawQ2.54
NoiseAvg:2.54,Stdev:0.04,Max:2.7,Min:2.4
Central-Avg:5540,Count:9
Corner+Avg:64,Count:32
Corner-Avg:5960,Count:32
BackgroundAvg:58.97,Stdev:0.25,Max:59.9,Min:58.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.821070373058
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-4_6hr-induced_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 ("Brownfield_1-4_6hr-induced_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: Brownfield_1-4_6hr-induced_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 6h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 um estradiol and incubated under constant light at 22°C further 6 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.998924255371
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:
RawQ2.46
NoiseAvg:2.53,Stdev:0.09,Max:2.8,Min:2.3
Central-Avg:5892,Count:9
Corner+Avg:62,Count:32
Corner-Avg:6773,Count:32
BackgroundAvg:58.61,Stdev:0.29,Max:59.4,Min:57.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.998924255371
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-5_6hr-induced_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 ("Brownfield_1-5_6hr-induced_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: Brownfield_1-5_6hr-induced_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 6h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 um estradiol and incubated under constant light at 22°C further 6 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.527977824211
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:2.80,Stdev:0.07,Max:3.1,Min:2.6
Central-Avg:5346,Count:9
Corner+Avg:78,Count:32
Corner-Avg:7098,Count:32
BackgroundAvg:57.80,Stdev:0.49,Max:58.6,Min:55.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.527977824211
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-6_6hr-induced_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Brownfield_1-6_6hr-induced_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Brownfield_1-6_6hr-induced_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 6h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 um estradiol and incubated under constant light at 22°C further 6 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.532631158829
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:
RawQ2.48
NoiseAvg:2.74,Stdev:0.07,Max:3.0,Min:2.4
Central-Avg:5939,Count:9
Corner+Avg:110,Count:32
Corner-Avg:6928,Count:32
BackgroundAvg:57.58,Stdev:0.24,Max:58.4,Min:56.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.532631158829
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-7_12hr-not-induced_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 ("Brownfield_1-7_12hr-not-induced_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: Brownfield_1-7_12hr-not-induced_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 12h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2 ul in 100 ml) and incubated under constant light at 22°C further 12 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.559041559696
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:2.73,Stdev:0.05,Max:2.9,Min:2.5
Central-Avg:5764,Count:9
Corner+Avg:76,Count:32
Corner-Avg:6987,Count:32
BackgroundAvg:57.45,Stdev:0.25,Max:58.0,Min:56.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.559041559696
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-8_12hr-not-induced_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 ("Brownfield_1-8_12hr-not-induced_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: Brownfield_1-8_12hr-not-induced_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 12h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2 ul in 100 ml) and incubated under constant light at 22°C further 12 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.620096206665
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:
RawQ2.35
NoiseAvg:2.52,Stdev:0.08,Max:2.8,Min:2.3
Central-Avg:5440,Count:9
Corner+Avg:70,Count:32
Corner-Avg:6442,Count:32
BackgroundAvg:56.08,Stdev:0.47,Max:57.7,Min:54.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.620096206665
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-9_12hr-not-induced_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Brownfield_1-9_12hr-not-induced_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Brownfield_1-9_12hr-not-induced_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 12h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2 ul in 100 ml) and incubated under constant light at 22°C further 12 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.676306545734
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:
RawQ2.28
NoiseAvg:2.48,Stdev:0.06,Max:2.7,Min:2.3
Central-Avg:5938,Count:9
Corner+Avg:73,Count:32
Corner-Avg:7401,Count:32
BackgroundAvg:56.39,Stdev:0.70,Max:58.1,Min:54.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.676306545734
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-10_12hr-induced_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 ("Brownfield_1-10_12hr-induced_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: Brownfield_1-10_12hr-induced_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 12h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 uM estradiol and incubated under constant light at 22°C further 12 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.651439249516
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:2.83,Stdev:0.14,Max:3.3,Min:2.6
Central-Avg:5361,Count:9
Corner+Avg:73,Count:32
Corner-Avg:6594,Count:32
BackgroundAvg:62.49,Stdev:1.02,Max:64.7,Min:59.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.651439249516
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-11_12hr-induced_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 ("Brownfield_1-11_12hr-induced_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: Brownfield_1-11_12hr-induced_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 12h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 uM estradiol and incubated under constant light at 22°C further 12 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.629570186138
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:
RawQ2.60
NoiseAvg:2.84,Stdev:0.06,Max:3.0,Min:2.7
Central-Avg:6463,Count:9
Corner+Avg:75,Count:32
Corner-Avg:7234,Count:32
BackgroundAvg:64.12,Stdev:0.30,Max:64.9,Min:63.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.629570186138
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-12_12hr-induced_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Brownfield_1-12_12hr-induced_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Brownfield_1-12_12hr-induced_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 12h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 uM estradiol and incubated under constant light at 22°C further 12 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.633438110352
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:
RawQ2.66
NoiseAvg:2.92,Stdev:0.17,Max:3.9,Min:2.7
Central-Avg:5935,Count:9
Corner+Avg:75,Count:32
Corner-Avg:7036,Count:32
BackgroundAvg:65.51,Stdev:0.39,Max:66.4,Min:64.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.633438110352
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-13_24hr-not-induced_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 ("Brownfield_1-13_24hr-not-induced_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: Brownfield_1-13_24hr-not-induced_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 24h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2 ul in 100 ml) and incubated under constant light at 22°C further 24 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.639715850353
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:
RawQ2.46
NoiseAvg:2.55,Stdev:0.08,Max:2.8,Min:2.2
Central-Avg:5868,Count:9
Corner+Avg:71,Count:32
Corner-Avg:6548,Count:32
BackgroundAvg:57.35,Stdev:0.30,Max:58.2,Min:56.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.639715850353
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-14_24hr-not-induced_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 ("Brownfield_1-14_24hr-not-induced_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: Brownfield_1-14_24hr-not-induced_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 24h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2 ul in 100 ml) and incubated under constant light at 22°C further 24 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.684973299503
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:2.53,Stdev:0.08,Max:2.8,Min:2.3
Central-Avg:4984,Count:9
Corner+Avg:62,Count:32
Corner-Avg:6159,Count:32
BackgroundAvg:59.48,Stdev:0.39,Max:60.3,Min:58.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.684973299503
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-15_24hr-not-induced_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Brownfield_1-15_24hr-not-induced_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Brownfield_1-15_24hr-not-induced_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 24h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing DMSO (2 ul in 100 ml) and incubated under constant light at 22°C further 24 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.487924009562
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:
RawQ2.74
NoiseAvg:3.16,Stdev:0.10,Max:3.5,Min:2.9
Central-Avg:6317,Count:9
Corner+Avg:69,Count:32
Corner-Avg:7123,Count:32
BackgroundAvg:69.94,Stdev:0.85,Max:71.9,Min:66.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.487924009562
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-16_24hr-induced_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 ("Brownfield_1-16_24hr-induced_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: Brownfield_1-16_24hr-induced_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 24h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 uM estradiol and incubated under constant light at 22°C further 24 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.504738986492
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:
RawQ2.58
NoiseAvg:3.01,Stdev:0.09,Max:3.3,Min:2.8
Central-Avg:6025,Count:9
Corner+Avg:80,Count:32
Corner-Avg:7977,Count:32
BackgroundAvg:64.41,Stdev:0.82,Max:66.1,Min:62.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.504738986492
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-17_24hr-induced_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 ("Brownfield_1-17_24hr-induced_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: Brownfield_1-17_24hr-induced_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 24h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 uM estradiol and incubated under constant light at 22°C further 24 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.739503920078
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:
RawQ2.46
NoiseAvg:2.52,Stdev:0.05,Max:2.7,Min:2.4
Central-Avg:5768,Count:9
Corner+Avg:80,Count:32
Corner-Avg:7750,Count:32
BackgroundAvg:57.89,Stdev:0.37,Max:59.0,Min:57.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.739503920078
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Brownfield_1-18_24hr-induced_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Brownfield_1-18_24hr-induced_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Brownfield_1-18_24hr-induced_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pMDC7DUO1
Stock Code:
Genetic Background: Col-0
Age: 24h
Growth Conditions:
Stratification3 days at 4°C on agar plate
sterilisation70% Ethanol/0.05% Tritin X-100 for 5 min 100% Ethanol for 10 min Air dry before plating
Growth protocolSeeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4°C for 3 days then plants grown under constant light at 22°C for 12 days before treatment began.
Growth substratePhytagar
LocationGrowth room
Average temperature22°C
Average humidity95%
Growth mediumMurashige & Skoog basal salt mixture
Developmental Stage:
Developmenatl stage(Source: Boye's Key - Paradigm Genetics)1.04
Genetic Variation: T-DNA mutation
Tissue: whole plant
in vivo Treatment:
Treatment protocolTwenty 12 day old seedlings (selected on hygromycin) were placed onto to fresh agar plates (phytagar, Murashige and Skoog basal salts, no sugar) containing 2 uM estradiol and incubated under constant light at 22°C further 24 h.
Additional Organism Information:
sampledescriptionSeedling with 4 true leaves plus cotyledons, root approximately 2 cm.
Other Information:
AlleleAt3g60460

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:0.605033576488
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:
RawQ2.53
NoiseAvg:2.63,Stdev:0.06,Max:2.8,Min:2.5
Central-Avg:7099,Count:9
Corner+Avg:91,Count:32
Corner-Avg:8908,Count:32
BackgroundAvg:61.92,Stdev:0.77,Max:64.2,Min:60.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.605033576488
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015


Problems? Comments? Suggestions? Contact the Affymetrix Team