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Experiment: Treatment of Arabidopsis with low concn. of nitrate

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-479

The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 μm nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism.

About the Experimenter

Name:Dr. Rongchen Wang
Head of Lab Name:Professor Nigel Crawford
Lab:
Address:University of California, San Diego
Division of Biological Sciences
9500 Gilman Drive, 0116
La Jolla, CA 92093-0116
USA
Postcode: 92093-0116
Country: USA
 
Telephone Number: 18585342519
Fax Number: 18585347108

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

About this Experiment

Experiment Type: compound_treatment_design;
Number of Slides:8
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
References:
ReferencePlant Physiol. 2003 June; 132(2): 556-567.
 
Other Information:

Slides in this Experiment

Hybridisation Set: Wang: Treatment of Arabidopsis with low concn. of nitrate_genome

Slide: Wang_1-1_WT-Col-250-micromolar-KCl-20-min-roots_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 ("Wang_1-1_WT-Col-250-micromolar-KCl-20-min-roots_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: Wang_1-1_WT-Col-250-micromolar-KCl-20-min-roots_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: Roots
Diseased: Control
in vivo Treatment:
Treatment250 µM KCl
Additional Organism Information:
Sample descriptionWT Col. 250 microM KCl 20 min, roots, replicate 1
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:0.389464
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:
RawQ4.90
NoiseAvg:6.76,Stdev:0.30,Max:8.0,Min:6.2
BackgroundAvg:132.68,Stdev:6.03,Max:152.0,Min:122.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.389464
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Wang_1-2_WT-Col-250-micromolar-K-nitrate-20-min-roots_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 ("Wang_1-2_WT-Col-250-micromolar-K-nitrate-20-min-roots_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: Wang_1-2_WT-Col-250-micromolar-K-nitrate-20-min-roots_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: Roots
Diseased: Treatment
in vivo Treatment:
Treatment250 µM KNO3
Additional Organism Information:
Sample descriptionWT Col. 250 microM KNO3 20 min, roots, replicate 1
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:0.39579
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:
RawQ4.91
NoiseAvg:6.59,Stdev:0.33,Max:7.6,Min:5.6
BackgroundAvg:128.02,Stdev:3.27,Max:135.0,Min:119.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.395790
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Wang_1-3_WT-Col-250-micromolar-KCl-20-min-roots_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 ("Wang_1-3_WT-Col-250-micromolar-KCl-20-min-roots_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: Wang_1-3_WT-Col-250-micromolar-KCl-20-min-roots_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: Roots
Diseased: Control
in vivo Treatment:
Treatment250 µM KCl
Additional Organism Information:
Sample descriptionWT Col. 250 microM KCl 20 min, roots, replicate 2
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:0.369463
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:
RawQ4.52
NoiseAvg:6.17,Stdev:0.36,Max:7.2,Min:5.3
BackgroundAvg:108.43,Stdev:3.49,Max:116.3,Min:99.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.369463
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Wang_1-4_WT-Col-250-micromolar-K-nitrate-20-min-roots_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 ("Wang_1-4_WT-Col-250-micromolar-K-nitrate-20-min-roots_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: Wang_1-4_WT-Col-250-micromolar-K-nitrate-20-min-roots_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: Roots
Diseased: Treatment
in vivo Treatment:
Treatment250 µM KNO3
Additional Organism Information:
Sample descriptionWT Col. 250 microM KNO3 20 min, roots, replicate 2
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:0.394014
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:
RawQ4.51
NoiseAvg:5.68,Stdev:0.23,Max:6.3,Min:5.0
BackgroundAvg:109.12,Stdev:2.53,Max:113.3,Min:102.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.394014
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Wang_1-5_Wild-type-Col-250-micromolar-KCL-20-min-shoots_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 ("Wang_1-5_Wild-type-Col-250-micromolar-KCL-20-min-shoots_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: Wang_1-5_Wild-type-Col-250-micromolar-KCL-20-min-shoots_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: shoots
Diseased: Control
in vivo Treatment:
Treatment250 µM KCl
Additional Organism Information:
Sample descriptionWT Col. 250 microM KCl 20 min, shoots, replicate 1
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:1.467058
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:
RawQ3.68
NoiseAvg:3.47,Stdev:0.18,Max:3.9,Min:3.1
BackgroundAvg:89.21,Stdev:2.70,Max:96.7,Min:83.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF1.467058
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Wang_1-6_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_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 ("Wang_1-6_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_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: Wang_1-6_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: shoots
Diseased: Treatment
in vivo Treatment:
Treatment250 µM KNO3
Additional Organism Information:
Sample descriptionWT Col. 250 microM KNO3 20 min, shoots, replicate 1
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:0.548938
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:
RawQ3.96
NoiseAvg:4.72,Stdev:0.28,Max:5.3,Min:3.9
BackgroundAvg:104.41,Stdev:4.30,Max:114.9,Min:93.5
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.548938
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Wang_1-7_Wild-type-Col-250-micromolar-KCL-20-min-shoots_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 ("Wang_1-7_Wild-type-Col-250-micromolar-KCL-20-min-shoots_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: Wang_1-7_Wild-type-Col-250-micromolar-KCL-20-min-shoots_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: shoots
Diseased: Control
in vivo Treatment:
Treatment250 µM KCl
Additional Organism Information:
Sample descriptionWT Col. 250 microM KCl 20 min, shoots, replicate 2
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:0.435676
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:
RawQ4.44
NoiseAvg:5.39,Stdev:0.18,Max:5.9,Min:4.7
BackgroundAvg:103.84,Stdev:1.82,Max:108.8,Min:100.5
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.435676
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Wang_1-8_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_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 ("Wang_1-8_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_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: Wang_1-8_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col.-0
Stock Code:
Growth Conditions:
Growth protocolArabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
Sterilisation protocolSeeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood.
Substrate sterilisation protocolIndividual component stock autoclaved separately; FeEDTA filter-sterilized
Developmental Stage:
Developmental stage10 days
Tissue: shoots
Diseased: Treatment
in vivo Treatment:
Treatment250 µM KNO3
Additional Organism Information:
Sample descriptionWT Col. 250 microM KNO3 20 min, shoots, replicate 2
Other Information:
ReferencePlant Physiol. 2003 June; 132(2): 556–567.

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:0.401121
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:
RawQ5.25
NoiseAvg:6.45,Stdev:0.22,Max:6.9,Min:5.7
BackgroundAvg:129.42,Stdev:2.81,Max:136.2,Min:123.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.401121
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015


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