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Experiment: Interaction Arabidopsis thaliana vs. Ralstonia solanacearum

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-447

Herein, whole genome expression analysis was conducted on rosettes of resistant and susceptible Arabidopsis thaliana accessions challenged with Ralstonia solanacearum. Two disease situations were considered: Col-5 plants inoculated with the virulent GMI1000 strain, as well as Nd-1 plants challenged with the same bacterial strain deleted of the avr PopP2 gene (DeltaPopP2), in both cases developing wilt disease symptoms. In contrast, Nd-1 plants challenged with GMI1000 are fully resistant to the pathogen and served as a control.Samples were harvested at the time of inoculation, as well as at 6, 12, 24 hours -at these times no symptoms were visible-, 5 days after inoculation when the first wilt symptoms became visible (25% of wilted leaves: disease index 1, D1), and finally 8 days after inoculation when 75 % of leaves were completely wilted (disease index 3, D3).

About the Experimenter

Name:Group leader Yves Marco
Head of Lab Name:Director of the institute Pascal Gamas
Lab:
Address:Laboratoire des Interactions Plantes-Microorganism
UMR CNRS-INRA 2594/441
Chemin de borde rouge
BP 52627
Postcode: 31326
Country: France
 
Telephone Number: 33561285509
Fax Number: 33561285061

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

About this Experiment

Experiment Type: time_series_design;pathogenicity_design
Number of Slides:34
 
Experimental Parameters:
parameterinfect
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Marco: Interaction Arabidopsis thaliana vs. Ralstonia solanacearum_genome

Slide: Marco_2-1_Col-0H_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 ("Marco_2-1_Col-0H_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: Marco_2-1_Col-0H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 0H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+8 bacteria per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample descriptionRosettes were harvested NucleoSpin RNAII kit (Macherey-Nagel, GmbH&Co.KG, Dueren, Germany) before inoculation.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.138821
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.42
NoiseAvg:2.45,Stdev:0.09,Max:2.6,Min:2.1
BackgroundAvg:53.95,Stdev:0.96,Max:56.4,Min:52.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.138821
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-2_Col-0H_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 ("Marco_2-2_Col-0H_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: Marco_2-2_Col-0H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 0H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+8 bacteria per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample descriptionRosettes were harvested NucleoSpin RNAII kit (Macherey-Nagel, GmbH&Co.KG, Dueren, Germany) before inoculation.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.139941
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:
RawQ3.52
NoiseAvg:3.82,Stdev:0.12,Max:4.2,Min:3.6
BackgroundAvg:82.32,Stdev:2.50,Max:86.8,Min:76.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.139941
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-3_Col-1000-6H_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 ("Marco_2-3_Col-1000-6H_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: Marco_2-3_Col-1000-6H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 6H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description6H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

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:0.965674
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:
RawQ2.90
NoiseAvg:3.21,Stdev:0.09,Max:3.6,Min:3.0
BackgroundAvg:65.85,Stdev:0.74,Max:68.1,Min:64.3
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.965674
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-4_Col-1000-6H_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 ("Marco_2-4_Col-1000-6H_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: Marco_2-4_Col-1000-6H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 6H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description6H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.140697
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:2.52,Stdev:0.07,Max:2.7,Min:2.3
BackgroundAvg:53.07,Stdev:0.68,Max:55.1,Min:51.3
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.140697
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-5_Col-1000-12H_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 ("Marco_2-5_Col-1000-12H_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: Marco_2-5_Col-1000-12H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 12H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description12H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.9206
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:
RawQ2.98
NoiseAvg:3.00,Stdev:0.09,Max:3.3,Min:2.8
BackgroundAvg:69.26,Stdev:2.22,Max:74.3,Min:65.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.920600
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-6_Col-1000-12H_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 ("Marco_2-6_Col-1000-12H_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: Marco_2-6_Col-1000-12H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 12H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description12H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.767454
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:
RawQ3.36
NoiseAvg:3.39,Stdev:0.09,Max:3.7,Min:3.0
BackgroundAvg:81.58,Stdev:1.22,Max:84.3,Min:78.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.767454
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-7_Col-1000-24H_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 ("Marco_2-7_Col-1000-24H_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: Marco_2-7_Col-1000-24H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 24H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.247239
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:
RawQ3.13
NoiseAvg:3.03,Stdev:0.06,Max:3.2,Min:2.9
BackgroundAvg:76.48,Stdev:0.96,Max:79.0,Min:74.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.247239
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-8_Col-1000-24H_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 ("Marco_2-8_Col-1000-24H_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: Marco_2-8_Col-1000-24H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: 24H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.804828
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:
RawQ3.05
NoiseAvg:3.21,Stdev:0.09,Max:3.5,Min:3.0
BackgroundAvg:69.21,Stdev:0.50,Max:70.5,Min:67.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.804828
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-9_Col-1000-D1_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 ("Marco_2-9_Col-1000-D1_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: Marco_2-9_Col-1000-D1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: D1 (5 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description5 days post inoculation. 25% of wilted leaves: disease index 1, D1.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.956615
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:2.28,Stdev:0.07,Max:2.5,Min:2.1
BackgroundAvg:49.34,Stdev:0.68,Max:50.9,Min:47.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.956615
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-10_Col-1000-D1_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 ("Marco_2-10_Col-1000-D1_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: Marco_2-10_Col-1000-D1_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: D1 (5 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description5 days post inoculation. 25% of wilted leaves: disease index 1, D1.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.811731
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:
RawQ3.45
NoiseAvg:3.37,Stdev:0.08,Max:3.6,Min:3.1
BackgroundAvg:87.83,Stdev:1.37,Max:91.1,Min:84.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.811731
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-11_Col-1000-D3_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 ("Marco_2-11_Col-1000-D3_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: Marco_2-11_Col-1000-D3_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: D3 (8 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description8 days post inoculation. 75% of wilted leaves: disease index 3, D3
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.061238
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:
RawQ2.77
NoiseAvg:2.71,Stdev:0.13,Max:3.1,Min:2.4
BackgroundAvg:61.80,Stdev:1.36,Max:65.7,Min:58.5
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.061238
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-12_Col-1000-D3_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 ("Marco_2-12_Col-1000-D3_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: Marco_2-12_Col-1000-D3_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-5
Stock Code:
Age: Time: D3 (8 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description8 days post inoculation. 75% of wilted leaves: disease index 3, D3
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.002347
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:
RawQ2.94
NoiseAvg:2.91,Stdev:0.10,Max:3.3,Min:2.7
BackgroundAvg:62.24,Stdev:1.23,Max:66.1,Min:59.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.002347
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-13_Nd-0H_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 ("Marco_2-13_Nd-0H_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: Marco_2-13_Nd-0H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 0H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

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:0.73932
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:
RawQ3.26
NoiseAvg:3.23,Stdev:0.11,Max:3.7,Min:2.9
BackgroundAvg:77.70,Stdev:1.43,Max:81.4,Min:74.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.739320
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-14_Nd-0H_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 ("Marco_2-14_Nd-0H_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: Marco_2-14_Nd-0H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 0H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.000072
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:
RawQ3.57
NoiseAvg:3.96,Stdev:0.47,Max:6.1,Min:3.1
BackgroundAvg:101.69,Stdev:12.51,Max:142.9,Min:80.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.000072
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-15_Nd-1000-6H_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 ("Marco_2-15_Nd-1000-6H_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: Marco_2-15_Nd-1000-6H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 6H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description6H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

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:0.964847
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:
RawQ2.98
NoiseAvg:3.25,Stdev:0.16,Max:3.8,Min:2.9
BackgroundAvg:68.85,Stdev:1.96,Max:73.6,Min:64.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.964847
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-16_Nd-1000-6H_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 ("Marco_2-16_Nd-1000-6H_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: Marco_2-16_Nd-1000-6H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 6H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description6H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.299363
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:
RawQ2.81
NoiseAvg:2.64,Stdev:0.07,Max:2.9,Min:2.5
BackgroundAvg:67.33,Stdev:1.17,Max:70.2,Min:64.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.299363
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-17_Nd-1000-12H_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 ("Marco_2-17_Nd-1000-12H_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: Marco_2-17_Nd-1000-12H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 12H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description12H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.774184
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:
RawQ3.28
NoiseAvg:3.74,Stdev:0.33,Max:4.8,Min:3.2
BackgroundAvg:71.48,Stdev:4.52,Max:78.6,Min:59.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.774184
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-18_Nd-1000-12H_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 ("Marco_2-18_Nd-1000-12H_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: Marco_2-18_Nd-1000-12H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 12H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants.
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description12H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.767944
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:
RawQ2.85
NoiseAvg:2.95,Stdev:0.08,Max:3.2,Min:2.7
BackgroundAvg:63.13,Stdev:0.95,Max:66.6,Min:61.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.767944
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-19_Nd-1000-24H_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 ("Marco_2-19_Nd-1000-24H_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: Marco_2-19_Nd-1000-24H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 24H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.357216
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:2.36,Stdev:0.10,Max:2.7,Min:2.1
BackgroundAvg:55.84,Stdev:1.19,Max:59.7,Min:53.5
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.357216
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-20_Nd-1000-24H_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 ("Marco_2-20_Nd-1000-24H_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: Marco_2-20_Nd-1000-24H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 24H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.019345
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:
RawQ2.85
NoiseAvg:2.69,Stdev:0.09,Max:2.9,Min:2.4
BackgroundAvg:62.63,Stdev:0.95,Max:65.4,Min:58.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.019345
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-21_Nd-1000-D1_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 ("Marco_2-21_Nd-1000-D1_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: Marco_2-21_Nd-1000-D1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D1 (5 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description5 days post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.887964
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:
RawQ3.35
NoiseAvg:3.51,Stdev:0.09,Max:3.8,Min:3.4
BackgroundAvg:79.62,Stdev:1.28,Max:84.1,Min:76.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.887964
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-22_Nd-1000-D1_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 ("Marco_2-22_Nd-1000-D1_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: Marco_2-22_Nd-1000-D1_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D1 (5 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description5 days post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.736813
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:
RawQ2.71
NoiseAvg:2.68,Stdev:0.07,Max:2.9,Min:2.4
BackgroundAvg:54.93,Stdev:0.83,Max:57.2,Min:53.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.736813
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-23_Nd-1000-D3_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 ("Marco_2-23_Nd-1000-D3_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: Marco_2-23_Nd-1000-D3_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D3 (8 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description8 days post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.08864
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:2.80,Stdev:0.07,Max:3.0,Min:2.6
BackgroundAvg:64.62,Stdev:1.61,Max:69.1,Min:60.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.088640
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-24_Nd-1000-D3_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 ("Marco_2-24_Nd-1000-D3_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: Marco_2-24_Nd-1000-D3_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D3 (8 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared on susceptible plants
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description8 days post inoculation.
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.768325
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:
RawQ3.05
NoiseAvg:3.01,Stdev:0.10,Max:3.3,Min:2.8
BackgroundAvg:68.12,Stdev:2.18,Max:72.5,Min:64.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.768325
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-25_Nd-DeltaPopP2-6H_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 ("Marco_2-25_Nd-DeltaPopP2-6H_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: Marco_2-25_Nd-DeltaPopP2-6H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 6H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocolRoot inoculations were performed according to the following protocol: approximately 2 cm was cut from the bottom of the Jiffy pot and the exposed roots of the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description6H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.880074
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:
RawQ3.54
NoiseAvg:3.66,Stdev:0.23,Max:5.2,Min:3.2
BackgroundAvg:81.34,Stdev:0.93,Max:83.9,Min:78.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.880074
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-26_Nd-DeltaPopP2-6H_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 ("Marco_2-26_Nd-DeltaPopP2-6H_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: Marco_2-26_Nd-DeltaPopP2-6H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 6H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description6H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.225882
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:
RawQ3.12
NoiseAvg:2.99,Stdev:0.12,Max:3.4,Min:2.7
BackgroundAvg:75.54,Stdev:0.93,Max:77.9,Min:72.3
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.225882
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-27_Nd-DeltaPopP2-12H_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 ("Marco_2-27_Nd-DeltaPopP2-12H_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: Marco_2-27_Nd-DeltaPopP2-12H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 12H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description12H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.973426
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:
RawQ3.01
NoiseAvg:2.97,Stdev:0.10,Max:3.3,Min:2.8
BackgroundAvg:69.71,Stdev:2.41,Max:75.8,Min:64.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.973426
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-28_Nd-DeltaPopP2-12H_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 ("Marco_2-28_Nd-DeltaPopP2-12H_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: Marco_2-28_Nd-DeltaPopP2-12H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 12H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description12H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.979321
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:
RawQ3.30
NoiseAvg:3.30,Stdev:0.12,Max:3.7,Min:2.9
BackgroundAvg:81.51,Stdev:2.04,Max:86.2,Min:77.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.979321
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-29_Nd-DeltaPopP2-24H_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 ("Marco_2-29_Nd-DeltaPopP2-24H_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: Marco_2-29_Nd-DeltaPopP2-24H_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 24H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.194914
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:
RawQ3.34
NoiseAvg:3.16,Stdev:0.10,Max:3.4,Min:2.9
BackgroundAvg:83.54,Stdev:1.01,Max:86.6,Min:80.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.194914
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-30_Nd-DeltaPopP2-24H_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 ("Marco_2-30_Nd-DeltaPopP2-24H_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: Marco_2-30_Nd-DeltaPopP2-24H_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: 24H
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description24H post inoculation
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.168606
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:
RawQ3.45
NoiseAvg:3.31,Stdev:0.14,Max:3.7,Min:2.9
BackgroundAvg:85.93,Stdev:1.05,Max:89.1,Min:83.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.168606
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-31_Nd-DeltaPopP2-D1_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 ("Marco_2-31_Nd-DeltaPopP2-D1_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: Marco_2-31_Nd-DeltaPopP2-D1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D1 (5 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description5 days post inoculation. 25% of wilted leaves: disease index 1, D1
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.857176
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:
RawQ3.27
NoiseAvg:3.11,Stdev:0.12,Max:3.5,Min:2.9
BackgroundAvg:77.08,Stdev:1.46,Max:81.6,Min:73.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.857176
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-32_Nd-DeltaPopP2-D1_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 ("Marco_2-32_Nd-DeltaPopP2-D1_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: Marco_2-32_Nd-DeltaPopP2-D1_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D1 (5 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description5 days post inoculation. 25% of wilted leaves: disease index 1, D1
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml.

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:0.886585
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:
RawQ3.49
NoiseAvg:3.54,Stdev:0.12,Max:3.8,Min:3.2
BackgroundAvg:86.52,Stdev:1.05,Max:88.8,Min:83.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.886585
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-33_Nd-DeltaPopP2-D3_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 ("Marco_2-33_Nd-DeltaPopP2-D3_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: Marco_2-33_Nd-DeltaPopP2-D3_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D3 (8 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description8 days post inoculation. 75% of wilted leaves: disease index 3, D3
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.253325
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:
RawQ3.34
NoiseAvg:3.17,Stdev:0.10,Max:3.4,Min:2.9
BackgroundAvg:81.60,Stdev:2.04,Max:86.6,Min:75.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.253325
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Marco_2-34_Nd-DeltaPopP2-D3_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 ("Marco_2-34_Nd-DeltaPopP2-D3_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: Marco_2-34_Nd-DeltaPopP2-D3_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Nd-1
Stock Code:
Age: Time: D3 (8 days)
Growth Conditions:
sterilisation20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.
Growth protocol(Source: Deslandes L, Pileur F, Liaubet L, Camut S, Can C, et al. (1998) Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum. Mol Plant Pathol Interact 11: 659-667.)Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20°C in a growth chamber were then transferred to Jiffy pots (Jiffy France, Lyon, France) and grown for 3 weeks at 22°C in short day conditions (10 h/14 h light/dark) under constant light at 500 µE s-1 m-2.
LocationGrowth Room
Growth substrate(Source: Jiffy-7 (Jiffy France, Lyon, France))Commercial soil
Developmental Stage:
Developmental stage(Source: Boyes Key)3.70
Tissue: Rosette
in vivo Treatment:
Treatment protocol1.00 10+7 bacteria (Ralstonia solanacearum GMI1000 DeltaPopP2) per ml. The plants were then transferred to a growth chamber at 25°C (16 h/8 h light/dark, constant light at 500 µE s-1 m-2) until symptoms appeared
Separation Technique: NucleoSpin RNA II kit (Macherey-Nagel, GmbH&Co.KG, Düren, Germany)
Other Information:
Sample description8 days post inoculation. 75% of wilted leaves: disease index 3, D3
Start timeWhen the plants were immersed for 3 min in a suspension containing 1.00 10+7 bacteria per ml

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.240204
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:
RawQ3.72
NoiseAvg:3.59,Stdev:0.15,Max:4.0,Min:3.2
BackgroundAvg:83.92,Stdev:5.22,Max:92.6,Min:72.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.240204
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015


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