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Experiment: Natural variation of auxin response

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-453

To assess natural variation of downstream auxin responses we subjected 7 different arabidopsis ecotypes to a time course of auxin treatments. 7d-old seedlings grown in liquid culture have been treated for 0, 30 min, 1h and 3h with 1 µM IAA.

About the Experimenter

Name: Marcel Quint
Head of Lab Name: Marcel Quint
Lab:
Address:Independent Junior Research Group
Leibniz Institute of Plant Biochemistry
Weinberg 3
06120 Halle
Postcode: 06120
Country: Germany
 

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

About this Experiment

Experiment Type: time_series_design; compound_treatment_design
Number of Slides:83
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
no-plants-pooled
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Quint: Natural variation of auxin response_genome

Slide: Quint_2-70_Col-0-3h_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-70_Col-0-3h_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: Quint_2-70_Col-0-3h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.758587598801
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:
RawQ2.23
NoiseAvg:2.39,Stdev:0.08,Max:2.6,Min:2.1
Central-Avg:7072,Count:9
Corner+Avg:72,Count:32
Corner-Avg:7577,Count:32
BackgroundAvg:53.00,Stdev:0.26,Max:53.8,Min:52.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.758587598801
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-69_Col-0-1h_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-69_Col-0-1h_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: Quint_2-69_Col-0-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.862626314163
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:2.27,Stdev:0.06,Max:2.4,Min:2.1
Central-Avg:6833,Count:9
Corner+Avg:71,Count:32
Corner-Avg:7870,Count:32
BackgroundAvg:52.39,Stdev:0.26,Max:52.9,Min:51.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.862626314163
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-68_Col-0-1h_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-68_Col-0-1h_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: Quint_2-68_Col-0-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.758789181709
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:
RawQ2.17
NoiseAvg:2.24,Stdev:0.04,Max:2.4,Min:2.1
Central-Avg:7518,Count:9
Corner+Avg:79,Count:32
Corner-Avg:8423,Count:32
BackgroundAvg:48.91,Stdev:0.28,Max:50.0,Min:48.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.758789181709
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-67_Col-0-1h_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 ("Quint_2-67_Col-0-1h_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: Quint_2-67_Col-0-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.562191843987
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.43
NoiseAvg:2.74,Stdev:0.07,Max:3.0,Min:2.6
Central-Avg:9576,Count:9
Corner+Avg:94,Count:32
Corner-Avg:9202,Count:32
BackgroundAvg:60.71,Stdev:0.54,Max:61.8,Min:59.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.562191843987
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-66_Col-0-30min_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 ("Quint_2-66_Col-0-30min_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: Quint_2-66_Col-0-30min_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.614804685116
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.43
NoiseAvg:2.69,Stdev:0.07,Max:2.9,Min:2.5
Central-Avg:9819,Count:9
Corner+Avg:101,Count:32
Corner-Avg:10482,Count:32
BackgroundAvg:57.61,Stdev:0.49,Max:58.6,Min:56.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.614804685116
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-65_Col-0-30min_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-65_Col-0-30min_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: Quint_2-65_Col-0-30min_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.572889626026
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:
RawQ2.47
NoiseAvg:2.91,Stdev:0.09,Max:3.2,Min:2.7
Central-Avg:9342,Count:9
Corner+Avg:95,Count:32
Corner-Avg:9581,Count:32
BackgroundAvg:63.08,Stdev:0.27,Max:63.7,Min:61.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.572889626026
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-64_Col-0-30min_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-64_Col-0-30min_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: Quint_2-64_Col-0-30min_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.690408170223
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:
RawQ2.30
NoiseAvg:2.44,Stdev:0.08,Max:2.8,Min:2.2
Central-Avg:8213,Count:9
Corner+Avg:87,Count:32
Corner-Avg:8503,Count:32
BackgroundAvg:55.41,Stdev:0.39,Max:56.3,Min:54.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.690408170223
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-63_Col-0-0h_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 ("Quint_2-63_Col-0-0h_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: Quint_2-63_Col-0-0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.816416203976
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:
RawQ2.20
NoiseAvg:2.28,Stdev:0.08,Max:2.5,Min:2.1
Central-Avg:8706,Count:9
Corner+Avg:89,Count:32
Corner-Avg:9883,Count:32
BackgroundAvg:52.30,Stdev:0.36,Max:53.3,Min:50.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.816416203976
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-62_Col-0-0h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-62_Col-0-0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-62_Col-0-0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.913061082363
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:
RawQ2.05
NoiseAvg:2.11,Stdev:0.04,Max:2.3,Min:2.0
Central-Avg:7648,Count:9
Corner+Avg:75,Count:32
Corner-Avg:8484,Count:32
BackgroundAvg:49.67,Stdev:0.17,Max:50.2,Min:49.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.913061082363
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-61_Col-0-0h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-61_Col-0-0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-61_Col-0-0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.804124772549
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.22
NoiseAvg:2.28,Stdev:0.05,Max:2.4,Min:2.1
Central-Avg:7047,Count:9
Corner+Avg:83,Count:32
Corner-Avg:8435,Count:32
BackgroundAvg:53.52,Stdev:0.24,Max:54.1,Min:53.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.804124772549
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-60_Fei-0-3h_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-60_Fei-0-3h_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: Quint_2-60_Fei-0-3h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.908304750919
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:
RawQ2.26
NoiseAvg:2.31,Stdev:0.05,Max:2.5,Min:2.1
Central-Avg:7942,Count:9
Corner+Avg:76,Count:32
Corner-Avg:8245,Count:32
BackgroundAvg:51.13,Stdev:0.32,Max:51.9,Min:50.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.908304750919
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-59_Fei-0-3h_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 ("Quint_2-59_Fei-0-3h_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: Quint_2-59_Fei-0-3h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.010051965714
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:
RawQ2.33
NoiseAvg:2.36,Stdev:0.03,Max:2.4,Min:2.3
Central-Avg:9807,Count:9
Corner+Avg:84,Count:32
Corner-Avg:10192,Count:32
BackgroundAvg:57.48,Stdev:0.44,Max:58.8,Min:56.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.010051965714
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-57_Fei-0-1h_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 ("Quint_2-57_Fei-0-1h_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: Quint_2-57_Fei-0-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.059380888939
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:
RawQ2.17
NoiseAvg:2.21,Stdev:0.08,Max:2.5,Min:2.0
Central-Avg:7813,Count:9
Corner+Avg:84,Count:32
Corner-Avg:9676,Count:32
BackgroundAvg:52.98,Stdev:0.42,Max:53.8,Min:51.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.059380888939
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-56_Fei-0-1h_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 ("Quint_2-56_Fei-0-1h_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: Quint_2-56_Fei-0-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.270211696625
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:
RawQ2.17
NoiseAvg:2.01,Stdev:0.09,Max:2.3,Min:1.8
Central-Avg:8112,Count:9
Corner+Avg:65,Count:32
Corner-Avg:8469,Count:32
BackgroundAvg:50.69,Stdev:0.59,Max:52.2,Min:49.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.270211696625
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-55_Fei-0-1h_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-55_Fei-0-1h_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: Quint_2-55_Fei-0-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.93554353714
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:
RawQ2.25
NoiseAvg:2.29,Stdev:0.04,Max:2.4,Min:2.1
Central-Avg:10622,Count:9
Corner+Avg:98,Count:32
Corner-Avg:11664,Count:32
BackgroundAvg:53.40,Stdev:0.37,Max:54.4,Min:52.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.935543537140
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-54_Fei-0-30min_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-54_Fei-0-30min_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: Quint_2-54_Fei-0-30min_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.70714455843
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:2.57,Stdev:0.07,Max:2.9,Min:2.4
Central-Avg:10945,Count:9
Corner+Avg:97,Count:32
Corner-Avg:11558,Count:32
BackgroundAvg:58.38,Stdev:0.39,Max:59.3,Min:57.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.707144558430
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-53_Fei-0-30min_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 ("Quint_2-53_Fei-0-30min_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: Quint_2-53_Fei-0-30min_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.620967030525
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:
RawQ2.52
NoiseAvg:2.82,Stdev:0.05,Max:3.0,Min:2.7
Central-Avg:8163,Count:9
Corner+Avg:87,Count:32
Corner-Avg:9118,Count:32
BackgroundAvg:63.44,Stdev:0.29,Max:64.0,Min:62.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.620967030525
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-52_Fei-0-30min_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 ("Quint_2-52_Fei-0-30min_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: Quint_2-52_Fei-0-30min_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.922633290291
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:
RawQ2.38
NoiseAvg:2.53,Stdev:0.07,Max:2.8,Min:2.3
Central-Avg:10649,Count:9
Corner+Avg:83,Count:32
Corner-Avg:10645,Count:32
BackgroundAvg:56.86,Stdev:0.27,Max:57.3,Min:55.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.922633290291
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-51_Fei-0-0h_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 ("Quint_2-51_Fei-0-0h_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: Quint_2-51_Fei-0-0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:1.072137594223
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.36
NoiseAvg:2.47,Stdev:0.08,Max:2.7,Min:2.3
Central-Avg:10737,Count:9
Corner+Avg:86,Count:32
Corner-Avg:10529,Count:32
BackgroundAvg:57.39,Stdev:0.35,Max:58.1,Min:56.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.072137594223
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-50_Fei-0-0h_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-50_Fei-0-0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-50_Fei-0-0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.728504240513
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.42
NoiseAvg:2.58,Stdev:0.08,Max:2.9,Min:2.4
Central-Avg:9902,Count:9
Corner+Avg:87,Count:32
Corner-Avg:10524,Count:32
BackgroundAvg:57.54,Stdev:0.48,Max:58.4,Min:55.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.728504240513
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-49_Fei-0-0h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-49_Fei-0-0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-49_Fei-0-0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Fei-0
Stock Code: CS28250
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.900358319283
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:
RawQ2.34
NoiseAvg:2.27,Stdev:0.07,Max:2.5,Min:2.1
Central-Avg:10119,Count:9
Corner+Avg:91,Count:32
Corner-Avg:11386,Count:32
BackgroundAvg:52.85,Stdev:0.43,Max:54.2,Min:52.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.900358319283
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-48_Bur-0-3h_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 ("Quint_2-48_Bur-0-3h_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: Quint_2-48_Bur-0-3h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.835244357586
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:2.73,Stdev:0.08,Max:3.0,Min:2.5
Central-Avg:11526,Count:9
Corner+Avg:102,Count:32
Corner-Avg:12098,Count:32
BackgroundAvg:63.61,Stdev:0.76,Max:65.3,Min:61.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.835244357586
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-47_Bur-0-3h_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 ("Quint_2-47_Bur-0-3h_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: Quint_2-47_Bur-0-3h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.203245282173
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.40
NoiseAvg:2.29,Stdev:0.07,Max:2.5,Min:2.1
Central-Avg:10104,Count:9
Corner+Avg:87,Count:32
Corner-Avg:11256,Count:32
BackgroundAvg:55.17,Stdev:0.58,Max:56.6,Min:53.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.203245282173
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-46_Bur-0-3h_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 ("Quint_2-46_Bur-0-3h_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: Quint_2-46_Bur-0-3h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.046093225479
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:2.31,Stdev:0.08,Max:2.6,Min:2.1
Central-Avg:8703,Count:9
Corner+Avg:85,Count:32
Corner-Avg:10953,Count:32
BackgroundAvg:54.34,Stdev:0.88,Max:56.2,Min:52.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.046093225479
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-45_Bur-0-1h_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-45_Bur-0-1h_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: Quint_2-45_Bur-0-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.90494799614
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:
RawQ2.38
NoiseAvg:2.37,Stdev:0.08,Max:2.7,Min:2.2
Central-Avg:10440,Count:9
Corner+Avg:91,Count:32
Corner-Avg:12039,Count:32
BackgroundAvg:54.29,Stdev:0.55,Max:56.0,Min:53.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.904947996140
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-44_Bur-0-1h_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 ("Quint_2-44_Bur-0-1h_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: Quint_2-44_Bur-0-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.679367184639
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:
RawQ2.30
NoiseAvg:2.14,Stdev:0.08,Max:2.6,Min:1.9
Central-Avg:7747,Count:9
Corner+Avg:75,Count:32
Corner-Avg:9441,Count:32
BackgroundAvg:52.15,Stdev:0.36,Max:53.2,Min:51.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.679367184639
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-43_Bur-0-1h_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 ("Quint_2-43_Bur-0-1h_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: Quint_2-43_Bur-0-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.023615956306
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:2.45,Stdev:0.08,Max:2.8,Min:2.2
Central-Avg:11061,Count:9
Corner+Avg:101,Count:32
Corner-Avg:12492,Count:32
BackgroundAvg:56.22,Stdev:0.22,Max:56.8,Min:55.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.023615956306
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-42_Bur-0-30min_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 ("Quint_2-42_Bur-0-30min_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: Quint_2-42_Bur-0-30min_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.927028715611
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:
RawQ2.76
NoiseAvg:2.87,Stdev:0.11,Max:3.2,Min:2.6
Central-Avg:12500,Count:9
Corner+Avg:106,Count:32
Corner-Avg:12932,Count:32
BackgroundAvg:64.38,Stdev:0.48,Max:65.9,Min:63.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.927028715611
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-41_Bur-0-30min_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-41_Bur-0-30min_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: Quint_2-41_Bur-0-30min_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.071078896523
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.48
NoiseAvg:2.50,Stdev:0.12,Max:3.2,Min:2.3
Central-Avg:10457,Count:9
Corner+Avg:105,Count:32
Corner-Avg:12590,Count:32
BackgroundAvg:57.26,Stdev:0.32,Max:57.9,Min:56.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.071078896523
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-40_Bur-0-30min_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 ("Quint_2-40_Bur-0-30min_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: Quint_2-40_Bur-0-30min_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.739810228348
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:
RawQ2.52
NoiseAvg:2.62,Stdev:0.06,Max:2.8,Min:2.5
Central-Avg:10704,Count:9
Corner+Avg:106,Count:32
Corner-Avg:12487,Count:32
BackgroundAvg:58.21,Stdev:0.41,Max:59.0,Min:57.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.739810228348
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-39_Bur-0h_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 ("Quint_2-39_Bur-0h_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: Quint_2-39_Bur-0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.79378080368
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:
RawQ2.72
NoiseAvg:2.77,Stdev:0.10,Max:3.2,Min:2.6
Central-Avg:11321,Count:9
Corner+Avg:116,Count:32
Corner-Avg:13047,Count:32
BackgroundAvg:61.89,Stdev:0.31,Max:62.7,Min:60.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.793780803680
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-38_Bur-0h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-38_Bur-0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-38_Bur-0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:1.064716100693
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:
RawQ2.23
NoiseAvg:2.32,Stdev:0.05,Max:2.4,Min:2.1
Central-Avg:9266,Count:9
Corner+Avg:88,Count:32
Corner-Avg:10903,Count:32
BackgroundAvg:52.22,Stdev:0.41,Max:53.3,Min:51.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.064716100693
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-37_Bur-0h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-37_Bur-0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-37_Bur-0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bur-0
Stock Code: N1028
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:1.413989305496
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:2.27,Stdev:0.09,Max:2.5,Min:2.0
Central-Avg:8308,Count:9
Corner+Avg:76,Count:32
Corner-Avg:9643,Count:32
BackgroundAvg:57.37,Stdev:0.69,Max:58.9,Min:55.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.413989305496
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-36_C24-3h_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 ("Quint_2-36_C24-3h_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: Quint_2-36_C24-3h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.506299257278
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:
RawQ2.02
NoiseAvg:1.94,Stdev:0.08,Max:2.2,Min:1.8
Central-Avg:7664,Count:9
Corner+Avg:62,Count:32
Corner-Avg:7941,Count:32
BackgroundAvg:47.93,Stdev:0.55,Max:48.9,Min:46.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.506299257278
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-35_C24-3h_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 ("Quint_2-35_C24-3h_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: Quint_2-35_C24-3h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.834471046925
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:
RawQ2.23
NoiseAvg:2.31,Stdev:0.06,Max:2.5,Min:2.1
Central-Avg:8577,Count:9
Corner+Avg:84,Count:32
Corner-Avg:9963,Count:32
BackgroundAvg:54.38,Stdev:0.37,Max:55.1,Min:53.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.834471046925
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-34_C24-3h_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 ("Quint_2-34_C24-3h_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: Quint_2-34_C24-3h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.891735196114
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:2.20,Stdev:0.08,Max:2.5,Min:1.9
Central-Avg:9159,Count:9
Corner+Avg:86,Count:32
Corner-Avg:10318,Count:32
BackgroundAvg:55.07,Stdev:0.34,Max:55.7,Min:54.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.891735196114
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-33_C24-1h_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 ("Quint_2-33_C24-1h_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: Quint_2-33_C24-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.114005327225
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:
RawQ1.97
NoiseAvg:1.81,Stdev:0.05,Max:2.0,Min:1.7
Central-Avg:9282,Count:9
Corner+Avg:75,Count:32
Corner-Avg:9728,Count:32
BackgroundAvg:46.30,Stdev:0.22,Max:46.8,Min:45.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.114005327225
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-32_C24-1h_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 ("Quint_2-32_C24-1h_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: Quint_2-32_C24-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.092938899994
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:
RawQ2.26
NoiseAvg:2.20,Stdev:0.07,Max:2.4,Min:2.0
Central-Avg:9520,Count:9
Corner+Avg:86,Count:32
Corner-Avg:10116,Count:32
BackgroundAvg:55.14,Stdev:0.40,Max:56.1,Min:54.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.092938899994
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-31_C24-1h_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-31_C24-1h_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: Quint_2-31_C24-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.041430711746
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:2.12,Stdev:0.05,Max:2.3,Min:2.0
Central-Avg:7458,Count:9
Corner+Avg:61,Count:32
Corner-Avg:7284,Count:32
BackgroundAvg:51.25,Stdev:0.25,Max:51.7,Min:50.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.041430711746
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-30_C24-30min_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-30_C24-30min_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: Quint_2-30_C24-30min_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.672377407551
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:
RawQ2.26
NoiseAvg:2.48,Stdev:0.06,Max:2.6,Min:2.3
Central-Avg:10083,Count:9
Corner+Avg:91,Count:32
Corner-Avg:10922,Count:32
BackgroundAvg:57.06,Stdev:0.40,Max:58.0,Min:55.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.672377407551
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-29_C24-30min_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-29_C24-30min_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: Quint_2-29_C24-30min_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.946765422821
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:0.06,Max:2.1,Min:1.8
Central-Avg:8681,Count:9
Corner+Avg:154,Count:32
Corner-Avg:9919,Count:32
BackgroundAvg:48.13,Stdev:0.29,Max:48.7,Min:47.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.946765422821
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-28_C24-30min_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-28_C24-30min_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: Quint_2-28_C24-30min_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.694297730923
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:
RawQ2.33
NoiseAvg:2.44,Stdev:0.06,Max:2.6,Min:2.2
Central-Avg:9003,Count:9
Corner+Avg:84,Count:32
Corner-Avg:10262,Count:32
BackgroundAvg:58.74,Stdev:0.37,Max:59.4,Min:57.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.694297730923
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-27_C24-0h_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 ("Quint_2-27_C24-0h_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: Quint_2-27_C24-0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.72043710947
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:
RawQ2.16
NoiseAvg:2.44,Stdev:0.17,Max:3.7,Min:2.2
Central-Avg:8862,Count:9
Corner+Avg:83,Count:32
Corner-Avg:10346,Count:32
BackgroundAvg:55.37,Stdev:0.46,Max:56.2,Min:53.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.720437109470
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-26_C24-0h_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-26_C24-0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-26_C24-0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.974559724331
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:
RawQ1.96
NoiseAvg:2.04,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:7172,Count:9
Corner+Avg:62,Count:32
Corner-Avg:7689,Count:32
BackgroundAvg:48.04,Stdev:0.25,Max:48.5,Min:47.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.974559724331
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-25_C24-0h_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-25_C24-0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-25_C24-0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: N906
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.772816181183
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:
RawQ2.26
NoiseAvg:2.36,Stdev:0.05,Max:2.6,Min:2.2
Central-Avg:6572,Count:9
Corner+Avg:65,Count:32
Corner-Avg:7668,Count:32
BackgroundAvg:53.46,Stdev:0.25,Max:54.3,Min:52.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.772816181183
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-24_Sha-3h_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 ("Quint_2-24_Sha-3h_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: Quint_2-24_Sha-3h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.978473365307
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:
RawQ2.29
NoiseAvg:2.28,Stdev:0.05,Max:2.4,Min:2.1
Central-Avg:6790,Count:9
Corner+Avg:74,Count:32
Corner-Avg:8534,Count:32
BackgroundAvg:53.88,Stdev:0.51,Max:55.4,Min:52.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.978473365307
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-23_Sha-3h_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 ("Quint_2-23_Sha-3h_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: Quint_2-23_Sha-3h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.681898534298
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:
RawQ2.23
NoiseAvg:2.31,Stdev:0.04,Max:2.5,Min:2.2
Central-Avg:7072,Count:9
Corner+Avg:66,Count:32
Corner-Avg:7915,Count:32
BackgroundAvg:54.10,Stdev:0.39,Max:55.1,Min:52.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.681898534298
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-22_Sha-3h_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-22_Sha-3h_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: Quint_2-22_Sha-3h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.728898108006
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:0.07,Max:2.7,Min:2.2
Central-Avg:6493,Count:9
Corner+Avg:72,Count:32
Corner-Avg:8078,Count:32
BackgroundAvg:53.67,Stdev:0.23,Max:54.4,Min:52.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.728898108006
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-21_Sha-1h_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-21_Sha-1h_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: Quint_2-21_Sha-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.945162296295
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:
RawQ1.99
NoiseAvg:1.99,Stdev:0.07,Max:2.2,Min:1.7
Central-Avg:6848,Count:9
Corner+Avg:61,Count:32
Corner-Avg:7513,Count:32
BackgroundAvg:48.18,Stdev:0.31,Max:48.8,Min:47.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.945162296295
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-20_Sha-1h_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-20_Sha-1h_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: Quint_2-20_Sha-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.959079802036
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:2.04,Stdev:0.04,Max:2.2,Min:1.9
Central-Avg:7531,Count:9
Corner+Avg:81,Count:32
Corner-Avg:8838,Count:32
BackgroundAvg:49.22,Stdev:0.27,Max:49.8,Min:48.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.959079802036
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-19_Sha-1h_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 ("Quint_2-19_Sha-1h_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: Quint_2-19_Sha-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.852990746498
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:
RawQ2.11
NoiseAvg:2.20,Stdev:0.05,Max:2.4,Min:2.0
Central-Avg:7764,Count:9
Corner+Avg:78,Count:32
Corner-Avg:8692,Count:32
BackgroundAvg:49.51,Stdev:0.26,Max:50.2,Min:48.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.852990746498
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-18_Sha-30min_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 ("Quint_2-18_Sha-30min_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: Quint_2-18_Sha-30min_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.892497360706
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:
RawQ2.34
NoiseAvg:2.44,Stdev:0.11,Max:3.1,Min:2.3
Central-Avg:7674,Count:9
Corner+Avg:71,Count:32
Corner-Avg:7990,Count:32
BackgroundAvg:58.88,Stdev:0.33,Max:59.5,Min:57.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.892497360706
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-17_Sha-30min_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-17_Sha-30min_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: Quint_2-17_Sha-30min_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.070312857628
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:
RawQ2.08
NoiseAvg:2.04,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:8077,Count:9
Corner+Avg:68,Count:32
Corner-Avg:8221,Count:32
BackgroundAvg:51.33,Stdev:0.20,Max:51.8,Min:50.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.070312857628
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-16_Sha-30min_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-16_Sha-30min_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: Quint_2-16_Sha-30min_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.935449123383
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:
RawQ2.14
NoiseAvg:2.24,Stdev:0.13,Max:3.2,Min:2.1
Central-Avg:6499,Count:9
Corner+Avg:73,Count:32
Corner-Avg:7964,Count:32
BackgroundAvg:50.00,Stdev:0.28,Max:50.8,Min:49.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.935449123383
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-15_Sha-0h_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 ("Quint_2-15_Sha-0h_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: Quint_2-15_Sha-0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.872827231884
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:
RawQ2.21
NoiseAvg:2.43,Stdev:0.07,Max:2.6,Min:2.2
Central-Avg:7715,Count:9
Corner+Avg:77,Count:32
Corner-Avg:8260,Count:32
BackgroundAvg:54.68,Stdev:0.37,Max:55.4,Min:53.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.872827231884
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-14_Sha-0h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-14_Sha-0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-14_Sha-0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:1.492274045944
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:
RawQ1.81
NoiseAvg:1.69,Stdev:0.05,Max:1.8,Min:1.5
Central-Avg:11601,Count:9
Corner+Avg:102,Count:32
Corner-Avg:12554,Count:32
BackgroundAvg:42.16,Stdev:0.40,Max:43.3,Min:41.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.492274045944
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-13_Sha-0h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-13_Sha-0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-13_Sha-0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Shakdara (Sha)
Stock Code: N929
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.911262214184
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:
RawQ2.20
NoiseAvg:2.24,Stdev:0.06,Max:2.4,Min:2.0
Central-Avg:7630,Count:9
Corner+Avg:70,Count:32
Corner-Avg:7857,Count:32
BackgroundAvg:52.61,Stdev:0.37,Max:53.3,Min:51.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.911262214184
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-12_Bay-0-3h_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-12_Bay-0-3h_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: Quint_2-12_Bay-0-3h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.677033126354
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:2.26,Stdev:0.06,Max:2.4,Min:2.1
Central-Avg:7517,Count:9
Corner+Avg:81,Count:32
Corner-Avg:8755,Count:32
BackgroundAvg:49.76,Stdev:0.25,Max:50.3,Min:48.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.677033126354
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-11_Bay-0-3h_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 ("Quint_2-11_Bay-0-3h_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: Quint_2-11_Bay-0-3h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.982653260231
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:2.26,Stdev:0.05,Max:2.4,Min:2.0
Central-Avg:8123,Count:9
Corner+Avg:69,Count:32
Corner-Avg:7562,Count:32
BackgroundAvg:51.92,Stdev:0.32,Max:52.8,Min:50.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.982653260231
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-10_Bay-0-3h_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 ("Quint_2-10_Bay-0-3h_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: Quint_2-10_Bay-0-3h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.082171916962
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:
RawQ2.11
NoiseAvg:2.07,Stdev:0.06,Max:2.3,Min:1.9
Central-Avg:7013,Count:9
Corner+Avg:64,Count:32
Corner-Avg:7693,Count:32
BackgroundAvg:50.74,Stdev:0.19,Max:51.2,Min:50.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.082171916962
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-9_Bay-0-1h_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 ("Quint_2-9_Bay-0-1h_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: Quint_2-9_Bay-0-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.015681862831
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:
RawQ1.91
NoiseAvg:1.92,Stdev:0.06,Max:2.1,Min:1.8
Central-Avg:7175,Count:9
Corner+Avg:64,Count:32
Corner-Avg:7408,Count:32
BackgroundAvg:47.22,Stdev:0.33,Max:48.0,Min:46.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.015681862831
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-8_Bay-0-1h_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-8_Bay-0-1h_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: Quint_2-8_Bay-0-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.118041157722
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:
RawQ2.05
NoiseAvg:2.04,Stdev:0.05,Max:2.2,Min:1.9
Central-Avg:6792,Count:9
Corner+Avg:65,Count:32
Corner-Avg:7886,Count:32
BackgroundAvg:48.65,Stdev:0.27,Max:49.4,Min:47.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.118041157722
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-7_Bay-0-1h_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 ("Quint_2-7_Bay-0-1h_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: Quint_2-7_Bay-0-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.912448525429
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:2.35,Stdev:0.07,Max:2.6,Min:2.1
Central-Avg:8469,Count:9
Corner+Avg:76,Count:32
Corner-Avg:8072,Count:32
BackgroundAvg:54.09,Stdev:0.37,Max:55.2,Min:53.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.912448525429
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-6_Bay-0-30min_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 ("Quint_2-6_Bay-0-30min_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: Quint_2-6_Bay-0-30min_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.369077205658
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:
RawQ2.12
NoiseAvg:2.06,Stdev:0.07,Max:2.3,Min:1.9
Central-Avg:6230,Count:9
Corner+Avg:69,Count:32
Corner-Avg:7576,Count:32
BackgroundAvg:50.29,Stdev:0.37,Max:51.2,Min:49.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.369077205658
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-5_Bay-0-30min_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 ("Quint_2-5_Bay-0-30min_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: Quint_2-5_Bay-0-30min_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.771148860455
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:
RawQ2.38
NoiseAvg:2.34,Stdev:0.06,Max:2.5,Min:2.2
Central-Avg:4903,Count:9
Corner+Avg:70,Count:32
Corner-Avg:6260,Count:32
BackgroundAvg:59.48,Stdev:0.36,Max:60.1,Min:58.1
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.771148860455
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-4_Bay-0-30min_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 ("Quint_2-4_Bay-0-30min_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: Quint_2-4_Bay-0-30min_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:1.685495018959
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:
RawQ1.93
NoiseAvg:1.80,Stdev:0.05,Max:2.0,Min:1.7
Central-Avg:5599,Count:9
Corner+Avg:68,Count:32
Corner-Avg:7215,Count:32
BackgroundAvg:44.24,Stdev:0.26,Max:44.9,Min:43.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.685495018959
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-3_Bay-0-0h_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-3_Bay-0-0h_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: Quint_2-3_Bay-0-0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.986456632614
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:
RawQ1.95
NoiseAvg:1.96,Stdev:0.04,Max:2.1,Min:1.8
Central-Avg:5525,Count:9
Corner+Avg:61,Count:32
Corner-Avg:6324,Count:32
BackgroundAvg:45.78,Stdev:0.22,Max:46.2,Min:45.2
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.986456632614
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-2_Bay-0-0h_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-2_Bay-0-0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-2_Bay-0-0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:1.252045869827
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:
RawQ1.92
NoiseAvg:1.89,Stdev:0.06,Max:2.0,Min:1.7
Central-Avg:6268,Count:9
Corner+Avg:57,Count:32
Corner-Avg:6603,Count:32
BackgroundAvg:44.90,Stdev:0.35,Max:45.5,Min:43.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.252045869827
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-1_Bay-0-0h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Quint_2-1_Bay-0-0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-1_Bay-0-0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bay-0 x Shahdara Core-Pop Bay-0 Parent
Stock Code: N57923
Genetic Background: Bay-0
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: recombinant inbred line
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:1.126876473427
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:
RawQ1.95
NoiseAvg:1.94,Stdev:0.04,Max:2.0,Min:1.7
Central-Avg:4398,Count:9
Corner+Avg:64,Count:32
Corner-Avg:5596,Count:32
BackgroundAvg:46.78,Stdev:0.17,Max:47.2,Min:46.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF1.126876473427
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-71_Col-0-3h_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 ("Quint_2-71_Col-0-3h_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: Quint_2-71_Col-0-3h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.906141579151
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:
RawQ2.08
NoiseAvg:2.20,Stdev:0.07,Max:2.4,Min:2.0
Central-Avg:8524,Count:9
Corner+Avg:72,Count:32
Corner-Avg:8641,Count:32
BackgroundAvg:50.47,Stdev:0.33,Max:51.1,Min:49.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.906141579151
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-72_Col-0-3h_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 ("Quint_2-72_Col-0-3h_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: Quint_2-72_Col-0-3h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.551703691483
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:
RawQ2.45
NoiseAvg:2.59,Stdev:0.07,Max:2.8,Min:2.4
Central-Avg:9438,Count:9
Corner+Avg:103,Count:32
Corner-Avg:10587,Count:32
BackgroundAvg:54.43,Stdev:0.35,Max:55.1,Min:53.0
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.551703691483
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-73_BI-1-0h_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_2-73_BI-1-0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-73_BI-1-0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.719029545784
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:2.30,Stdev:0.07,Max:2.6,Min:2.0
Central-Avg:8633,Count:9
Corner+Avg:95,Count:32
Corner-Avg:10019,Count:32
BackgroundAvg:51.49,Stdev:0.25,Max:52.0,Min:50.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.719029545784
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-74_BI-1-0h_Rep2_ATH1

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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 ("Quint_2-74_BI-1-0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Quint_2-74_BI-1-0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.952198445797
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:
RawQ2.14
NoiseAvg:2.29,Stdev:0.05,Max:2.5,Min:2.2
Central-Avg:8555,Count:9
Corner+Avg:85,Count:32
Corner-Avg:9006,Count:32
BackgroundAvg:51.08,Stdev:0.49,Max:51.9,Min:49.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.952198445797
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-75_BI-1-0h_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 ("Quint_2-75_BI-1-0h_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: Quint_2-75_BI-1-0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start procedureprior to treatment

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:0.979058146477
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ2.39
NoiseAvg:2.52,Stdev:0.09,Max:2.8,Min:2.3
Central-Avg:8916,Count:9
Corner+Avg:95,Count:32
Corner-Avg:9584,Count:32
BackgroundAvg:54.46,Stdev:0.34,Max:55.3,Min:53.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.979058146477
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-76_BI-1-30min_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 ("Quint_2-76_BI-1-30min_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: Quint_2-76_BI-1-30min_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.476162105799
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:3.16,Stdev:0.09,Max:3.5,Min:2.9
Central-Avg:9291,Count:9
Corner+Avg:105,Count:32
Corner-Avg:10367,Count:32
BackgroundAvg:65.78,Stdev:0.42,Max:67.1,Min:64.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.476162105799
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-77_BI-1-30min_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Quint_2-77_BI-1-30min_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: Quint_2-77_BI-1-30min_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.906683385372
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:2.41,Stdev:0.07,Max:2.7,Min:2.2
Central-Avg:8772,Count:9
Corner+Avg:80,Count:32
Corner-Avg:9153,Count:32
BackgroundAvg:51.68,Stdev:0.26,Max:52.2,Min:50.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.906683385372
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-78_BI-1-30min_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 ("Quint_2-78_BI-1-30min_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: Quint_2-78_BI-1-30min_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.640442013741
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:
RawQ2.33
NoiseAvg:2.65,Stdev:0.07,Max:2.8,Min:2.5
Central-Avg:11370,Count:9
Corner+Avg:108,Count:32
Corner-Avg:11748,Count:32
BackgroundAvg:55.31,Stdev:0.36,Max:56.2,Min:54.4
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.640442013741
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-79_BI-1-1h_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 ("Quint_2-79_BI-1-1h_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: Quint_2-79_BI-1-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.68486559391
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:2.49,Stdev:0.07,Max:2.7,Min:2.3
Central-Avg:9298,Count:9
Corner+Avg:91,Count:32
Corner-Avg:9235,Count:32
BackgroundAvg:54.62,Stdev:0.56,Max:55.8,Min:53.5
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.684865593910
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-80_BI-1-1h_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 ("Quint_2-80_BI-1-1h_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: Quint_2-80_BI-1-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.879945933819
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:
RawQ2.15
NoiseAvg:2.25,Stdev:0.10,Max:2.6,Min:2.0
Central-Avg:7987,Count:9
Corner+Avg:82,Count:32
Corner-Avg:8991,Count:32
BackgroundAvg:51.43,Stdev:0.52,Max:52.5,Min:49.9
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.879945933819
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-81_BI-1-1h_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 ("Quint_2-81_BI-1-1h_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: Quint_2-81_BI-1-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.79598659277
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:
RawQ2.30
NoiseAvg:2.41,Stdev:0.06,Max:2.6,Min:2.2
Central-Avg:7557,Count:9
Corner+Avg:83,Count:32
Corner-Avg:8551,Count:32
BackgroundAvg:52.09,Stdev:0.22,Max:52.7,Min:51.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.795986592770
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-82_BI-1-3h_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 ("Quint_2-82_BI-1-3h_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: Quint_2-82_BI-1-3h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.891917943954
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:2.33,Stdev:0.06,Max:2.5,Min:2.2
Central-Avg:8043,Count:9
Corner+Avg:83,Count:32
Corner-Avg:8863,Count:32
BackgroundAvg:52.00,Stdev:0.37,Max:53.0,Min:50.8
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.891917943954
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-83_BI-1-3h_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 ("Quint_2-83_BI-1-3h_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: Quint_2-83_BI-1-3h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.656175017357
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:2.58,Stdev:0.07,Max:2.8,Min:2.4
Central-Avg:8148,Count:9
Corner+Avg:87,Count:32
Corner-Avg:9254,Count:32
BackgroundAvg:58.60,Stdev:0.68,Max:59.7,Min:56.7
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.656175017357
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Quint_2-84_BI-1-3h_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 ("Quint_2-84_BI-1-3h_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: Quint_2-84_BI-1-3h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Bl-1
Stock Code: N968
Age: 7 days
Growth Conditions:
StratificationAfter sterilization, seeds were incubated in sterile water in the dark for 5 days at 4°C prior to cultivation
SterilisationSeed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification
ProtocolSterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 °C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.
ReferenceReference for ATS medium: Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080
Substrate Sterilising Procedureautoclaved
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
MediumOwn medium: ATS medium according to Lincoln et al. (1990)
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: Indole-3-acetic acid (IAA)(Duchefa, Netherlands)was applied at a final concentration of 1µM
Additional Organism Information:
Sample DescriptionRNA was extracted from a pool of 7 d old seedlings cultivated in liquid ATS
Other Information:
Timecourse start proceduretime of IAA application

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:0.686773717403
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:
RawQ2.30
NoiseAvg:2.51,Stdev:0.05,Max:2.7,Min:2.4
Central-Avg:10042,Count:9
Corner+Avg:104,Count:32
Corner-Avg:11549,Count:32
BackgroundAvg:54.85,Stdev:0.21,Max:55.5,Min:54.3
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG2
Gamma2H0.003
SF0.686773717403
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015


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