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Experiment: Arabidopsis E2F target genes

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-337

Entry into the S phase of the cell cycle is controlled by the E2F transcitption factors that induce the transcription of genes required for cell cycle progression and DNA replication. To identify E2F target genes of Arabidopsis on a genome-wide scale, the transcriptome of wild-type plants was compared with that one of plants ectopically expressing the E2Fa-DPa genes. In four independent experiments, E2Fa-DPa overexpressing plants were grown side-to-side with wild type (Col-0) plants. RNA was extracted from 6-day-old seedlings. Each biological sample was harvested and processed independently, and finally all probed individually to Affymetrix ATH1 microarrays, resulting into 8 hybridization signals for each probeset.

About the Experimenter

Name:Dr. Lieven De Veylder
Head of Lab Name:Prof. Dirk Inze
Lab:
Address:Technologiepark 927
B-9052 Gent
Postcode: B-9052
Country: Belgium
 
Telephone Number: +32 9 3313961
Fax Number: +32 9 3313809

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: genetic_modification_design
Number of Slides:8
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:
GEO accessionGSE5529

Slides in this Experiment

Hybridisation Set: De Veylder: Arabidopsis E2F target genes_genome

Slide: De Veylder_1-1_wildtype_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("De Veylder_1-1_wildtype_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:

BioSource 1 Information

BioSource Name: De Veylder_1-1_wildtype_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.858083
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:
RawQ2.39
NoiseAvg:2.49,Stdev:0.11,Max:2.9,Min:2.3
BackgroundAvg:55.90,Stdev:1.07,Max:58.7,Min:53.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.858083
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: De Veylder_1-2_wildtype_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("De Veylder_1-2_wildtype_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:

BioSource 1 Information

BioSource Name: De Veylder_1-2_wildtype_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.864574
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.50
NoiseAvg:2.72,Stdev:0.09,Max:3.0,Min:2.4
BackgroundAvg:61.12,Stdev:1.19,Max:63.1,Min:57.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.864574
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: De Veylder_1-3_wildtype_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("De Veylder_1-3_wildtype_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:

BioSource 1 Information

BioSource Name: De Veylder_1-3_wildtype_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.8126
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ1.44
NoiseAvg:1.78,Stdev:0.05,Max:1.9,Min:1.6
BackgroundAvg:38.35,Stdev:0.23,Max:38.9,Min:37.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.812600
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: De Veylder_1-4_wildtype_Rep4_ATH1

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

Summary Information

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

  • Extract 1 ("De Veylder_1-4_wildtype_Rep4_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:

BioSource 1 Information

BioSource Name: De Veylder_1-4_wildtype_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.703586
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ1.56
NoiseAvg:2.01,Stdev:0.10,Max:2.4,Min:1.8
BackgroundAvg:43.02,Stdev:0.27,Max:43.8,Min:42.3
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.703586
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: De Veylder_1-5_E2Fa-Dpa_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("De Veylder_1-5_E2Fa-Dpa_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:

BioSource 1 Information

BioSource Name: De Veylder_1-5_E2Fa-Dpa_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.645168
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ1.41
NoiseAvg:1.67,Stdev:0.04,Max:1.8,Min:1.5
BackgroundAvg:36.94,Stdev:0.22,Max:37.5,Min:36.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.645168
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: De Veylder_1-6_E2Fa-Dpa_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("De Veylder_1-6_E2Fa-Dpa_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:

BioSource 1 Information

BioSource Name: De Veylder_1-6_E2Fa-Dpa_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.761136
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.22
NoiseAvg:2.28,Stdev:0.07,Max:2.5,Min:2.2
BackgroundAvg:52.47,Stdev:0.60,Max:54.0,Min:51.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.761136
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: De Veylder_1-7_E2Fa-Dpa_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("De Veylder_1-7_E2Fa-Dpa_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:

BioSource 1 Information

BioSource Name: De Veylder_1-7_E2Fa-Dpa_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.708378
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:
RawQ2.51
NoiseAvg:2.70,Stdev:0.09,Max:2.9,Min:2.5
BackgroundAvg:63.01,Stdev:2.85,Max:67.9,Min:56.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.708378
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: De Veylder_1-8_E2Fa-Dpa_Rep4_ATH1

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

Summary Information

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

  • Extract 1 ("De Veylder_1-8_E2Fa-Dpa_Rep4_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:

BioSource 1 Information

BioSource Name: De Veylder_1-8_E2Fa-Dpa_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Seed sterilisationSeeds were surface sterilized with 15% sodium hypochloride for 10 min
Growth protocolPlants were grown on 1x Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands) and 0.6% plant tissue culture agar (LabM, Bury, UK) at 22°C and 65 ?E?m 2?s 1 radiation in a 16 h light/8 h dark photoperiod.
LocationGrowth chamber
Growth substrate(Source: 0.8)Agar
Growth medium1x Murashige and Skoog basal salt mixture
Sample descriptionTotal seedlings were harvested 6 days after germiantion (8 days after sowing)
Tissue: whole plant
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.751022
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ1.53
NoiseAvg:1.88,Stdev:0.03,Max:2.0,Min:1.8
BackgroundAvg:39.39,Stdev:0.15,Max:39.8,Min:38.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.751022
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015


Problems? Comments? Suggestions? Contact the Affymetrix Team