NASC's International Affymetrix Service

AI logo

NASCArrays

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

Experiment: Investigating the molecular response of Arabidopsis to combined nematode and dehydration stress using the Affymetrix ATH1 microarray.

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-489

Plants respond to stress by activating differential signalling pathways leading to tolerance and resistance. Response to individual abiotic and biotic stresses has been well studied. There are key elements in common between the two pathways including the interplay of plant hormones, transcription factors and signal transduction cascades. It is thought that the two pathways may also act antagonistically in order to prioritise stress response, a process governed by the hormones abscisic acid and jasmonic acid (Anderson et al., 2004 Plant Cell 16: 3460-3479). Little is known about the molecular effect of simultaneous abiotic and biotic stress in plants. This study will characterise transcriptome changes in response to combined abiotic and biotic stress, namely dehydration and nematode infection. The response to these stresses will be analysed in roots and leaves. Arabidopsis Col-0 plants were grown on half MS media for 18 days (growth stage 1.08-1.12, Boyes et al., 2001 Plant Cell 13:1499-1510). Half the plants were challenged with rigorously sterilised, infective Heterodera schachtii nematodes as described before (Fuller et al., 2007 Molecular Plant Pathology 8: 595-609). Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. At 10 days post infection (growth stage 3.2-3.5, Boyes et al, 2001) half the plants from each group were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar in the growth cabinet for a further 30 minutes before harvesting the tissue. Control plants were lifted off the agar and then immediately pla ced back in the growth cabinet for 45 minutes. Root and leaf tissue was harvested separately from each of the four treatment groups and RNA isolated using an RNeasy plant RNA preparation kit (Qiagen). The experiment will be carried out three times to provide biological replicates.

About the Experimenter

Name:Miss Nicola Spencer-Jones
Head of Lab Name:Dr. Peter Urwin
Lab:
Address:9.91c Manton
Centre for Plant Sciences
Faculty of Biological Sciences
University of Leeds
Woodhouse Lane
Postcode: LS2 9JT
Country: UK
 
Telephone Number: 01133433035

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: pathogenicity_design
Number of Slides:24
 
Experimental Parameters:
parameterinfect
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Spencer-Jones: Investigating the molecular response of Arabidopsis to combined nematode and dehydration stress using the Affymetrix ATH1 microarray._genome

Slide: Spencer-Jones_1-24_H.schachtii-dehydrated-root_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-24_H.schachtii-dehydrated-root_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-24_H.schachtii-dehydrated-root_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 30 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.986221253872
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.66
NoiseAvg:2.71,Stdev:0.09,Max:2.9,Min:2.4
Central-Avg:6213,Count:9
Corner+Avg:66,Count:32
Corner-Avg:7587,Count:32
BackgroundAvg:63.13,Stdev:0.25,Max:64.1,Min:62.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.986221253872
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-23_H.schachtii-dehydrated-root_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 ("Spencer-Jones_1-23_H.schachtii-dehydrated-root_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: Spencer-Jones_1-23_H.schachtii-dehydrated-root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.983768582344
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.18
NoiseAvg:2.24,Stdev:0.06,Max:2.4,Min:2.1
Central-Avg:7846,Count:9
Corner+Avg:77,Count:32
Corner-Avg:9496,Count:32
BackgroundAvg:50.96,Stdev:0.46,Max:52.3,Min:50.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.983768582344
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-22_H.schachtii-dehydrated-root_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 ("Spencer-Jones_1-22_H.schachtii-dehydrated-root_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: Spencer-Jones_1-22_H.schachtii-dehydrated-root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20°C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium used was Murashige & Skoog Medium, including vitamins. Product number: MO222.0025. 10g/litre sucrose was added.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Root
in vivo Treatment: These plants were innoculated with nematodes and then treated with dehydration stress. At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treated plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. 10 days later plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, leaf material was separated from the roots of the plant and was immediately frozen in liquid nitrogen. Root RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.431947827339
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:
RawQ2.62
NoiseAvg:2.90,Stdev:0.08,Max:3.2,Min:2.7
Central-Avg:9219,Count:9
Corner+Avg:86,Count:32
Corner-Avg:10072,Count:32
BackgroundAvg:63.65,Stdev:0.49,Max:64.7,Min:62.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.431947827339
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-21_H.schachtii-dehydrated-leaf_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-21_H.schachtii-dehydrated-leaf_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-21_H.schachtii-dehydrated-leaf_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.079324126244
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:
RawQ2.65
NoiseAvg:2.75,Stdev:0.09,Max:3.0,Min:2.6
Central-Avg:7225,Count:9
Corner+Avg:74,Count:32
Corner-Avg:8485,Count:32
BackgroundAvg:62.61,Stdev:0.80,Max:65.6,Min:61.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.079324126244
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-20_H.schachtii-dehydrated-leaf_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 ("Spencer-Jones_1-20_H.schachtii-dehydrated-leaf_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: Spencer-Jones_1-20_H.schachtii-dehydrated-leaf_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.746051490307
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:
RawQ3.11
NoiseAvg:3.60,Stdev:0.41,Max:6.3,Min:3.1
Central-Avg:7274,Count:9
Corner+Avg:82,Count:32
Corner-Avg:8857,Count:32
BackgroundAvg:76.90,Stdev:1.72,Max:81.4,Min:73.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.746051490307
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-17_H.schachtii-root_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 ("Spencer-Jones_1-17_H.schachtii-root_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: Spencer-Jones_1-17_H.schachtii-root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.726236879826
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:
RawQ2.24
NoiseAvg:2.43,Stdev:0.05,Max:2.6,Min:2.4
Central-Avg:7613,Count:9
Corner+Avg:75,Count:32
Corner-Avg:8748,Count:32
BackgroundAvg:55.28,Stdev:0.62,Max:57.1,Min:53.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.726236879826
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-16_H.schachtii-root_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 ("Spencer-Jones_1-16_H.schachtii-root_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: Spencer-Jones_1-16_H.schachtii-root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20°C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium used was Murashige & Skoog Medium, including vitamins. Product number: MO222.0025. 10g/litre sucrose was added.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Root
in vivo Treatment: These plants were innoculated with nematodes, but were not treated with dehydration stress. At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treated plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, leaf material was separated from the roots of the plant and was immediately frozen in liquid nitrogen. Root RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.350594043732
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:3.35,Stdev:0.10,Max:3.8,Min:3.1
Central-Avg:8999,Count:9
Corner+Avg:90,Count:32
Corner-Avg:10253,Count:32
BackgroundAvg:72.60,Stdev:0.54,Max:73.6,Min:70.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.350594043732
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-18_H.schachtii-root_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-18_H.schachtii-root_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-18_H.schachtii-root_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.548267900944
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.37
NoiseAvg:2.71,Stdev:0.06,Max:2.9,Min:2.4
Central-Avg:9093,Count:9
Corner+Avg:81,Count:32
Corner-Avg:9688,Count:32
BackgroundAvg:59.88,Stdev:0.32,Max:60.5,Min:58.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.548267900944
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-15_H.schachtii-leaf_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-15_H.schachtii-leaf_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-15_H.schachtii-leaf_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.038707256317
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.07
NoiseAvg:2.05,Stdev:0.07,Max:2.3,Min:1.9
Central-Avg:7502,Count:9
Corner+Avg:70,Count:32
Corner-Avg:8376,Count:32
BackgroundAvg:48.99,Stdev:0.33,Max:49.6,Min:47.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.038707256317
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-19_H.schachtii-dehydrated-leaf_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 ("Spencer-Jones_1-19_H.schachtii-dehydrated-leaf_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: Spencer-Jones_1-19_H.schachtii-dehydrated-leaf_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20°C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium used was Murashige & Skoog Medium, including vitamins. Product number: MO222.0025. 10g/litre sucrose was added.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Leaf
in vivo Treatment: These plants were innoculated with nematodes and then treated with dehydration stress. At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treated plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. 10 days later plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, leaf material was separated from the roots of the plant and was immediately frozen in liquid nitrogen. Leaf RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.510970771313
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:
RawQ2.63
NoiseAvg:3.03,Stdev:0.06,Max:3.2,Min:2.8
Central-Avg:10690,Count:9
Corner+Avg:97,Count:32
Corner-Avg:11238,Count:32
BackgroundAvg:66.33,Stdev:0.50,Max:67.9,Min:64.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.510970771313
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-14_H.schachtii-leaf_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 ("Spencer-Jones_1-14_H.schachtii-leaf_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: Spencer-Jones_1-14_H.schachtii-leaf_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treatment plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. Control plants were mock inoculated with sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.025144815445
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ1.94
NoiseAvg:1.99,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:7186,Count:9
Corner+Avg:74,Count:32
Corner-Avg:8604,Count:32
BackgroundAvg:46.51,Stdev:0.45,Max:47.7,Min:45.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.025144815445
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-13_H.schachtii-leaf_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 ("Spencer-Jones_1-13_H.schachtii-leaf_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: Spencer-Jones_1-13_H.schachtii-leaf_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20°C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium used was Murashige & Skoog Medium, including vitamins. Product number: MO222.0025. 10g/litre sucrose was added.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Leaf
in vivo Treatment: These plants were innoculated with nematodes, but were not treated with dehydration stress. At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and treatment groups. Roots of these treated plants were infected with H. schachtii J2 stage nematodes. Each plant was treated with a total of c. 175 juveniles in sterile distilled water at five separate infection points. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, leaf material was separated from the roots of the plant and was immediately frozen in liquid nitrogen. Leaf RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.581076323986
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:
RawQ2.70
NoiseAvg:3.03,Stdev:0.06,Max:3.3,Min:2.8
Central-Avg:8434,Count:9
Corner+Avg:85,Count:32
Corner-Avg:9430,Count:32
BackgroundAvg:68.60,Stdev:0.46,Max:69.3,Min:66.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.581076323986
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-12_Dehydrated-root_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-12_Dehydrated-root_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-12_Dehydrated-root_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.629791736603
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:
RawQ2.27
NoiseAvg:2.37,Stdev:0.03,Max:2.5,Min:2.3
Central-Avg:9257,Count:9
Corner+Avg:78,Count:32
Corner-Avg:9759,Count:32
BackgroundAvg:52.89,Stdev:0.27,Max:53.7,Min:51.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.629791736603
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-11_Dehydrated-root_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 ("Spencer-Jones_1-11_Dehydrated-root_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: Spencer-Jones_1-11_Dehydrated-root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.940364420414
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.10
NoiseAvg:2.08,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:7681,Count:9
Corner+Avg:69,Count:32
Corner-Avg:8502,Count:32
BackgroundAvg:48.76,Stdev:0.31,Max:49.4,Min:47.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.940364420414
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-10_Dehydrated-root_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 ("Spencer-Jones_1-10_Dehydrated-root_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: Spencer-Jones_1-10_Dehydrated-root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:
RNAQCNo
RNAReceivedNo

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:0.326867878437
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:
RawQ2.89
NoiseAvg:3.62,Stdev:0.13,Max:4.0,Min:3.4
Central-Avg:9709,Count:9
Corner+Avg:97,Count:32
Corner-Avg:10380,Count:32
BackgroundAvg:75.24,Stdev:0.78,Max:76.9,Min:72.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.326867878437
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-9_Dehydrated-leaf_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-9_Dehydrated-leaf_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-9_Dehydrated-leaf_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.707927525043
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.22
NoiseAvg:2.41,Stdev:0.05,Max:2.6,Min:2.2
Central-Avg:9040,Count:9
Corner+Avg:89,Count:32
Corner-Avg:10414,Count:32
BackgroundAvg:52.51,Stdev:0.26,Max:53.0,Min:51.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.707927525043
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-8_Dehydrated-leaf_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 ("Spencer-Jones_1-8_Dehydrated-leaf_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: Spencer-Jones_1-8_Dehydrated-leaf_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
in vivo Treatment: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the green parts of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.606038212776
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.28
NoiseAvg:2.49,Stdev:0.06,Max:2.6,Min:2.4
Central-Avg:7654,Count:9
Corner+Avg:81,Count:32
Corner-Avg:9081,Count:32
BackgroundAvg:54.87,Stdev:0.25,Max:55.4,Min:54.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.606038212776
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-7_Dehydrated-leaf_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 ("Spencer-Jones_1-7_Dehydrated-leaf_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: Spencer-Jones_1-7_Dehydrated-leaf_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium used was Murashige & Skoog Medium, including vitamins. Product number: MO222.0025. 10g/litre sucrose was added.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Leaf
in vivo Treatment: These plants were not innoculated with nematodes, but were treated with dehydration stress. At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants the plants were subjected to dehydration stress. Plants were carefully lifted off the agar and desiccated for 15 minutes in plastic Petri dishes under a clean stream of air. During this time the plants lost 10-15% of their fresh weight. Plants were returned to the agar and put back in the growth cabinet for a further 30 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, leaf material was separated from the roots of the plant and was immediately frozen in liquid nitrogen. Leaf RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.439558625221
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:3.13,Stdev:0.13,Max:3.7,Min:2.9
Central-Avg:9163,Count:9
Corner+Avg:101,Count:32
Corner-Avg:10761,Count:32
BackgroundAvg:66.93,Stdev:0.33,Max:67.5,Min:65.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.439558625221
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-6_Control-root_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-6_Control-root_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-6_Control-root_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
Additional Organism Information:
Sample DescriptionAt growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.527762770653
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.41
NoiseAvg:2.61,Stdev:0.06,Max:2.8,Min:2.4
Central-Avg:9257,Count:9
Corner+Avg:88,Count:32
Corner-Avg:10420,Count:32
BackgroundAvg:58.47,Stdev:0.47,Max:60.0,Min:57.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.527762770653
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-5_Control-root_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 ("Spencer-Jones_1-5_Control-root_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: Spencer-Jones_1-5_Control-root_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: roots
Additional Organism Information:
Sample DescriptionAt growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.439067602158
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.22
NoiseAvg:2.58,Stdev:0.09,Max:2.8,Min:2.3
Central-Avg:8404,Count:9
Corner+Avg:94,Count:32
Corner-Avg:10218,Count:32
BackgroundAvg:53.01,Stdev:0.37,Max:53.9,Min:52.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.439067602158
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-4_Control-root_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 ("Spencer-Jones_1-4_Control-root_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: Spencer-Jones_1-4_Control-root_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium used was Murashige & Skoog Medium, including vitamins. Product number: MO222.0025. 10g/litre sucrose was added.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Root
in vivo Treatment: These control plants underwent similar handling procedures to the treated plants in order to minimise differences in gene response: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, root material was separated from the leaves of the plant and was immediately frozen in liquid nitrogen. Root RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.356008261442
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:
RawQ2.97
NoiseAvg:3.88,Stdev:0.45,Max:6.8,Min:3.3
Central-Avg:8174,Count:9
Corner+Avg:91,Count:32
Corner-Avg:10016,Count:32
BackgroundAvg:78.53,Stdev:0.74,Max:79.7,Min:76.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.356008261442
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-1_Control-leaf_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 ("Spencer-Jones_1-1_Control-leaf_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: Spencer-Jones_1-1_Control-leaf_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium used was Murashige & Skoog Medium, including vitamins. Product number: MO222.0025. 10g/litre sucrose was added.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Leaf
in vivo Treatment: These control plants underwent similar handling procedures to the treated plants in order to minimise differences in gene response: At growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Additional Organism Information:
Sample DescriptionFollowing mock dehydration treatment and 45 minutes back in the growth cabinet, leaf material was separated from the roots of the plant and was immediately frozen in liquid nitrogen. RNA was pooled from 40 plants.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.53755825758
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.41
NoiseAvg:2.72,Stdev:0.11,Max:3.1,Min:2.5
Central-Avg:8108,Count:9
Corner+Avg:92,Count:32
Corner-Avg:10314,Count:32
BackgroundAvg:58.59,Stdev:0.82,Max:60.6,Min:57.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.537558257580
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-2_Control-leaf_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 ("Spencer-Jones_1-2_Control-leaf_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: Spencer-Jones_1-2_Control-leaf_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
Additional Organism Information:
Sample DescriptionAt growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.995900273323
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.19
NoiseAvg:2.16,Stdev:0.04,Max:2.3,Min:2.0
Central-Avg:7817,Count:9
Corner+Avg:78,Count:32
Corner-Avg:8991,Count:32
BackgroundAvg:49.56,Stdev:0.36,Max:50.4,Min:48.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.995900273323
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Spencer-Jones_1-3_Control-leaf_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Spencer-Jones_1-3_Control-leaf_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Spencer-Jones_1-3_Control-leaf_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 28 days
Growth Conditions:
StratificationAfter sterilisation the seeds were kept in sterile distilled water at 4ºC in the dark for 48 hours.
SterilisationSeeds were soaked for 30 minutes in sterile distilled water, followed by 95% ethanol for two minutes and 10% bleach for a further five minutes. The seeds were washed five times in sterile distilled water.
ProtocolWild-type Col-0 Arabidopsis plants were grown in square Petri dishes on half strength MS media supplemented with 10 g/L sucrose. Growth took place in Sanyo Environmental Test Chambers at 20 °C under 16-h/8-h light/dark cycles with average light intensity of 140 µmol/m2/s. Plates were kept upright to facilitate downward growth of the roots.
Percentage Agrose1
Substrate Sterilising ProcedureMedia was sterilised in a pressure cooker at 121ºC for 20 minutes.
Plant Spacing4 plants per 10cm plate
Temperature20 °C average, 20 °C day, 20 °C night
Humidity30 % average, 30 % day, 30 % night
MediumMurashige & Skoog basal salt mixture. Modifications: The medium was Murashige & Skoog with vitamins. 10 g/l sucrose was added to the medium.
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 140 µmol/m2/sµEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: leaves
Additional Organism Information:
Sample DescriptionAt growth stage 1.08–1.12 (Boyes et al., 2001) plants were randomly allocated into control and nematode treatment groups. These were control plants therefore were mock inoculated with 175µl sterile water. 10 days later plants from each group were randomly allocated again into control and dehydration treatment groups. These were control plants so instead of dehydration, plants were carefully lifted off the plate and then immediately placed back on the agar and returned to the growth cabinet for 45 minutes before harvesting the tissue.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.870860874653
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.22
NoiseAvg:2.27,Stdev:0.08,Max:2.5,Min:2.1
Central-Avg:5850,Count:9
Corner+Avg:72,Count:32
Corner-Avg:8623,Count:32
BackgroundAvg:52.93,Stdev:0.17,Max:53.4,Min:52.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.870860874653
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015


Problems? Comments? Suggestions? Contact the Affymetrix Team