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Experiment: Transcriptomic studies to understand the circadian clock temperature buffering mechanism

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-147

The circadian clock temporally orchestrates many physiological and developmental processes. The accuracy with which it co-ordinates these events with the daily light/dark cycle gives an organism a competitive advantage. For a clock to remain accurate it must be buffered against unpredictable fluctuations in temperature. We have identified the gene GI as playing a role in this buffering process. To understand the underlying temperature buffering mechanism we aim to investigate, in gi and WT changes in the transcriptome.The Arabidopsis (wt (WS) and gi11 (WS)) seeds will be sterilised and then plated on MS 3% sucrose plates. The seeds will be cold treated for 2 days and then germinated and grown under 12h light 12h dark cycles at 22°C for 7 days. On the seventh day plants will be transferred to constant light at a range of temperatures (12°C, 17°C, 22°C and 27°C). RNA will be isolated over one circadian cycle on the third day of adaptation and then pooled, (prior to pooling the RNA will be analysed on a denaturing gel and using real time PCR and quantified using Quant-itä RNA assay). The pooling over one circadian cycle is essential when you are comparing WT to a mutant with an altered period. Using this approach we aim to identify temperature-regulated transcripts and transcripts that are mis-regulated in gi at specific temperatures.This transcriptomic study is funded by the BBSRC.

About the Experimenter

Name:Mr Peter Gould
Head of Lab Name:Dr Anthony Hall
Lab: University of Liverpool
Institute: University of Liverpool
Address:University of Liverpool
School of Biological Sciences
Bioscience Building
Crown Street
Liverpool
Postcode: L69 7ZB
Country: UK
 
Telephone Number: 0151 7954555
Fax Number: 0151 7954410

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:
Number of Slides:24
 
Experimental Parameters:
parametergene_knock_out
parameterchange_temperature
Quality Control Measures Taken:
no-plants-pooled1000
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Gould_Mutant

Slide: Gould_1-5_WT-GI-12degrees_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 ("Gould_1-5_WT-GI-12degrees_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: Gould_1-5_WT-GI-12degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.452387
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:
RawQ2.99
NoiseAvg:4.46,Stdev:0.14,Max:5.0,Min:4.0
BackgroundAvg:75.23,Stdev:1.29,Max:78.2,Min:72.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.452387
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-6_WT-GI-17degrees_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 ("Gould_1-6_WT-GI-17degrees_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: Gould_1-6_WT-GI-17degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.350651
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ3.41
NoiseAvg:5.36,Stdev:0.33,Max:7.4,Min:4.5
BackgroundAvg:92.41,Stdev:1.91,Max:97.6,Min:88.2
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.350651
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-7_WT-GI-22degrees_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 ("Gould_1-7_WT-GI-22degrees_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: Gould_1-7_WT-GI-22degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.340909
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ3.83
NoiseAvg:5.86,Stdev:0.18,Max:6.4,Min:5.4
BackgroundAvg:107.60,Stdev:1.39,Max:110.8,Min:104.5
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.340909
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-8_WT-GI-27degrees_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 ("Gould_1-8_WT-GI-27degrees_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: Gould_1-8_WT-GI-27degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.381197
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ3.43
NoiseAvg:5.08,Stdev:0.22,Max:5.9,Min:4.7
BackgroundAvg:92.94,Stdev:1.41,Max:95.5,Min:89.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.381197
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-17_GI11-MUT-12degrees_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 ("Gould_1-17_GI11-MUT-12degrees_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: Gould_1-17_GI11-MUT-12degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 12 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.861942
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.253334
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.234426
Spike_AFFX-r2-Bs-dap_5_signal1.038440
NoiseAvg:4.98,Std:0.15,Min:4.5,Max:5.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal4.078291
#P12216
Spike_AFFX-r2-Bs-phe_M_signal1.541961
Corner-Avg:8165,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal37.743629
Spike_AFFX-r2-Ec-bioB_3_signal53.920963
Spike_AFFX-r2-Bs-lys_M_signal9.345718
Spike_AFFX-r2-P1-cre_3_signal3469.506836
Spike_AFFX-r2-Bs-lys_3-5-ratio2.074293
Spike_AFFX-r2-Bs-dap_M_signal0.722200
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.349029
Spike_AFFX-r2-Ec-bioB_avg-signal45.115204
Spike_AFFX-r2-Bs-thr_avg-signal4.972416
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal531.909241
Spike_AFFX-r2-Bs-phe_5_signal3.727760
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal731.719482
RawQ4.116008
Spike_AFFX-r2-Bs-lys_5_signal0.382576
Signal(A)12.241452
%A43.608067
Signal(All)150.830490
Corner+Avg:96,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal141.634003
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal4.815937
Spike_AFFX-r2-Ec-bioD_avg-signal631.814331
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P53.555458
Spike_AFFX-r2-Bs-lys_avg-signal3.934196
Spike_AFFX-r2-P1-cre_avg-signal3118.864990
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.836475
Spike_AFFX-r2-Bs-thr_3_signal1.423443
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal3.361886
Spike_AFFX-r2-Bs-dap_3_signal1.502436
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.375647
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal151.103165
#M647
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal2.074293
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.937333
Spike_AFFX-r2-Bs-thr_M_signal9.415514
Signal(P)269.600159
Spike_AFFX-r2-Bs-phe_3-5-ratio1.291912
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:6786,Count:9
Spike_AFFX-r2-P1-cre_5_signal2768.223145
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9947
Signal(M)39.014496
BackgroundAvg:116.11,Std:2.80,Min:108.3,Max:121.6
Spike_AFFX-r2-Ec-bioC_avg-signal146.368591
Spike_AFFX-r2-Bs-dap_avg-signal1.087692
Spike_AFFX-r2-Bs-dap_3-5-ratio1.446819
Spike_AFFX-r2-Ec-bioB_5_signal43.681011
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.861942
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-18_GI11-MUT-17degrees_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 ("Gould_1-18_GI11-MUT-17degrees_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: Gould_1-18_GI11-MUT-17degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 17 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.782404
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.256452
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.332991
Spike_AFFX-r2-Bs-dap_5_signal0.730614
NoiseAvg:4.36,Std:0.13,Min:4.1,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.451681
#P12934
Spike_AFFX-r2-Bs-phe_M_signal0.500802
Corner-Avg:8551,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal37.992119
Spike_AFFX-r2-Ec-bioB_3_signal19.646084
Spike_AFFX-r2-Bs-lys_M_signal4.456319
Spike_AFFX-r2-P1-cre_3_signal2480.856934
Spike_AFFX-r2-Bs-lys_3-5-ratio4.743820
Spike_AFFX-r2-Bs-dap_M_signal2.560239
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.147747
Spike_AFFX-r2-Ec-bioB_avg-signal38.879017
Spike_AFFX-r2-Bs-thr_avg-signal6.624041
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal316.105713
Spike_AFFX-r2-Bs-phe_5_signal0.371953
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal417.382721
RawQ3.809089
Spike_AFFX-r2-Bs-lys_5_signal0.664183
Signal(A)10.834413
%A40.512932
Signal(All)144.448181
Corner+Avg:90,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal105.487991
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal5.198139
Spike_AFFX-r2-Ec-bioD_avg-signal366.744202
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P56.703201
Spike_AFFX-r2-Bs-lys_avg-signal3.288108
Spike_AFFX-r2-P1-cre_avg-signal2227.675049
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.783867
Spike_AFFX-r2-Bs-thr_3_signal9.700388
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.023631
Spike_AFFX-r2-Bs-dap_3_signal1.774673
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.320390
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal96.238907
#M635
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal4.743820
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.096105
Spike_AFFX-r2-Bs-thr_M_signal1.720053
Signal(P)245.303925
Spike_AFFX-r2-Bs-phe_3-5-ratio5.198139
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:7100,Count:9
Spike_AFFX-r2-P1-cre_5_signal1974.493286
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9241
Signal(M)34.615879
BackgroundAvg:104.69,Std:1.74,Min:99.3,Max:108.1
Spike_AFFX-r2-Ec-bioC_avg-signal100.863449
Spike_AFFX-r2-Bs-dap_avg-signal1.688509
Spike_AFFX-r2-Bs-dap_3-5-ratio1.774673
Spike_AFFX-r2-Ec-bioB_5_signal58.998844
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.782404
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-19_GI11-MUT-22degrees_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 ("Gould_1-19_GI11-MUT-22degrees_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: Gould_1-19_GI11-MUT-22degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 22 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.862025
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.367635
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.507102
Spike_AFFX-r2-Bs-dap_5_signal7.604733
NoiseAvg:4.97,Std:0.15,Min:4.7,Max:5.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal23.800661
#P12536
Spike_AFFX-r2-Bs-phe_M_signal1.748390
Corner-Avg:8628,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal30.488199
Spike_AFFX-r2-Ec-bioB_3_signal19.733109
Spike_AFFX-r2-Bs-lys_M_signal0.509803
Spike_AFFX-r2-P1-cre_3_signal2704.719238
Spike_AFFX-r2-Bs-lys_3-5-ratio2.793459
Spike_AFFX-r2-Bs-dap_M_signal1.114588
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.076743
Spike_AFFX-r2-Ec-bioB_avg-signal29.711601
Spike_AFFX-r2-Bs-thr_avg-signal8.841599
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal362.586151
Spike_AFFX-r2-Bs-phe_5_signal0.980781
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal498.672607
RawQ4.054721
Spike_AFFX-r2-Bs-lys_5_signal1.773078
Signal(A)13.350463
%A42.082420
Signal(All)144.204697
Corner+Avg:80,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal125.636223
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal2.323102
Spike_AFFX-r2-Ec-bioD_avg-signal430.629395
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P54.958351
Spike_AFFX-r2-Bs-lys_avg-signal2.411967
Spike_AFFX-r2-P1-cre_avg-signal2341.190430
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.959229
Spike_AFFX-r2-Bs-thr_3_signal1.826544
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal1.684091
Spike_AFFX-r2-Bs-dap_3_signal0.791662
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.375322
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal125.312241
#M675
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal4.953020
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.002585
Spike_AFFX-r2-Bs-thr_M_signal0.897594
Signal(P)249.951736
Spike_AFFX-r2-Bs-phe_3-5-ratio2.323102
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:7631,Count:9
Spike_AFFX-r2-P1-cre_5_signal1977.661865
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9599
Signal(M)41.130531
BackgroundAvg:118.07,Std:1.98,Min:112.6,Max:122.5
Spike_AFFX-r2-Ec-bioC_avg-signal125.474228
Spike_AFFX-r2-Bs-dap_avg-signal3.170327
Spike_AFFX-r2-Bs-dap_3-5-ratio0.104101
Spike_AFFX-r2-Ec-bioB_5_signal38.913498
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.862025
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-20_GI11-MUT-27degrees_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 ("Gould_1-20_GI11-MUT-27degrees_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: Gould_1-20_GI11-MUT-27degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 27 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.865808
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.257990
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.957208
Spike_AFFX-r2-Bs-dap_5_signal0.439441
NoiseAvg:4.86,Std:0.13,Min:4.5,Max:5.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.926269
#P13013
Spike_AFFX-r2-Bs-phe_M_signal2.521975
Corner-Avg:8594,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal7.619026
Spike_AFFX-r2-Ec-bioB_3_signal31.563274
Spike_AFFX-r2-Bs-lys_M_signal9.870974
Spike_AFFX-r2-P1-cre_3_signal1985.852661
Spike_AFFX-r2-Bs-lys_3-5-ratio10.393592
Spike_AFFX-r2-Bs-dap_M_signal0.767442
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.323283
Spike_AFFX-r2-Ec-bioB_avg-signal24.052200
Spike_AFFX-r2-Bs-thr_avg-signal6.021935
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal248.358810
Spike_AFFX-r2-Bs-phe_5_signal2.669913
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal335.183594
RawQ4.040166
Spike_AFFX-r2-Bs-lys_5_signal1.328684
Signal(A)12.684876
%A40.267426
Signal(All)139.498077
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal91.072044
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal1.164466
Spike_AFFX-r2-Ec-bioD_avg-signal291.771210
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P57.049541
Spike_AFFX-r2-Bs-lys_avg-signal8.336488
Spike_AFFX-r2-P1-cre_avg-signal1782.222168
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.683034
Spike_AFFX-r2-Bs-thr_3_signal2.885711
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.118785
Spike_AFFX-r2-Bs-dap_3_signal0.722060
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.349594
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal90.118202
#M612
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal13.809804
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.010584
Spike_AFFX-r2-Bs-thr_M_signal6.253823
Signal(P)233.719604
Spike_AFFX-r2-Bs-phe_3-5-ratio0.436144
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:7111,Count:9
Spike_AFFX-r2-P1-cre_5_signal1578.591797
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9185
Signal(M)39.293076
BackgroundAvg:105.96,Std:1.97,Min:101.0,Max:110.5
Spike_AFFX-r2-Ec-bioC_avg-signal90.595123
Spike_AFFX-r2-Bs-dap_avg-signal0.642981
Spike_AFFX-r2-Bs-dap_3-5-ratio0.722060
Spike_AFFX-r2-Ec-bioB_5_signal32.974297
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.865808
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-21_GI11-MUT-12degrees_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 ("Gould_1-21_GI11-MUT-12degrees_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: Gould_1-21_GI11-MUT-12degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 12 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Waternone
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.381237
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.431808
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.665966
Spike_AFFX-r2-Bs-dap_5_signal0.464367
NoiseAvg:4.71,Std:0.26,Min:4.1,Max:5.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.131910
#P14024
Spike_AFFX-r2-Bs-phe_M_signal2.442187
Corner-Avg:11858,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal19.743446
Spike_AFFX-r2-Ec-bioB_3_signal22.422611
Spike_AFFX-r2-Bs-lys_M_signal3.108284
Spike_AFFX-r2-P1-cre_3_signal2157.314209
Spike_AFFX-r2-Bs-lys_3-5-ratio7.672420
Spike_AFFX-r2-Bs-dap_M_signal0.282520
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.345543
Spike_AFFX-r2-Ec-bioB_avg-signal25.278452
Spike_AFFX-r2-Bs-thr_avg-signal1.289839
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal263.527679
Spike_AFFX-r2-Bs-phe_5_signal0.820001
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal406.710327
RawQ3.191883
Spike_AFFX-r2-Bs-lys_5_signal0.641836
Signal(A)8.237019
%A35.966682
Signal(All)139.840530
Corner+Avg:135,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal73.089607
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal1.096200
Spike_AFFX-r2-Ec-bioD_avg-signal335.119019
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.481808
Spike_AFFX-r2-Bs-lys_avg-signal3.807513
Spike_AFFX-r2-P1-cre_avg-signal1832.010498
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.551512
Spike_AFFX-r2-Bs-thr_3_signal0.736667
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal1.452796
Spike_AFFX-r2-Bs-dap_3_signal0.377549
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.543331
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal82.654236
#M582
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal7.672420
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.884281
Spike_AFFX-r2-Bs-thr_M_signal1.000941
Signal(P)221.527893
Spike_AFFX-r2-Bs-phe_3-5-ratio1.096200
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10104,Count:9
Spike_AFFX-r2-P1-cre_5_signal1506.706787
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8204
Signal(M)26.595942
BackgroundAvg:73.12,Std:1.44,Min:69.2,Max:76.6
Spike_AFFX-r2-Ec-bioC_avg-signal77.871918
Spike_AFFX-r2-Bs-dap_avg-signal0.374812
Spike_AFFX-r2-Bs-dap_3-5-ratio0.377549
Spike_AFFX-r2-Ec-bioB_5_signal33.669304
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.381237
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-22_GI11-MUT-17degrees_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 ("Gould_1-22_GI11-MUT-17degrees_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: Gould_1-22_GI11-MUT-17degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 17 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Waternone
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.507769
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.368124
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.479743
Spike_AFFX-r2-Bs-dap_5_signal0.294725
NoiseAvg:4.10,Std:0.13,Min:3.8,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.882375
#P13639
Spike_AFFX-r2-Bs-phe_M_signal2.639650
Corner-Avg:11856,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal27.298634
Spike_AFFX-r2-Ec-bioB_3_signal21.086550
Spike_AFFX-r2-Bs-lys_M_signal0.737194
Spike_AFFX-r2-P1-cre_3_signal2715.361572
Spike_AFFX-r2-Bs-lys_3-5-ratio0.451071
Spike_AFFX-r2-Bs-dap_M_signal3.145237
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.220074
Spike_AFFX-r2-Ec-bioB_avg-signal30.779671
Spike_AFFX-r2-Bs-thr_avg-signal4.451548
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal364.330383
Spike_AFFX-r2-Bs-phe_5_signal1.041739
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal570.230286
RawQ2.954227
Spike_AFFX-r2-Bs-lys_5_signal5.627246
Signal(A)9.471514
%A37.531784
Signal(All)142.470627
Corner+Avg:123,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal122.935875
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal3.597888
Spike_AFFX-r2-Ec-bioD_avg-signal467.280334
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P59.793949
Spike_AFFX-r2-Bs-lys_avg-signal2.967576
Spike_AFFX-r2-P1-cre_avg-signal2350.047607
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.674266
Spike_AFFX-r2-Bs-thr_3_signal2.174853
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.426426
Spike_AFFX-r2-Bs-dap_3_signal1.380517
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.565146
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal118.589088
#M610
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal2.538289
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.036654
Spike_AFFX-r2-Bs-thr_M_signal1.297417
Signal(P)230.973862
Spike_AFFX-r2-Bs-phe_3-5-ratio3.453732
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:9600,Count:9
Spike_AFFX-r2-P1-cre_5_signal1984.733643
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8561
Signal(M)30.191317
BackgroundAvg:68.76,Std:0.82,Min:66.8,Max:70.6
Spike_AFFX-r2-Ec-bioC_avg-signal120.762482
Spike_AFFX-r2-Bs-dap_avg-signal1.606826
Spike_AFFX-r2-Bs-dap_3-5-ratio1.380517
Spike_AFFX-r2-Ec-bioB_5_signal43.953827
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.507769
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-23_GI11-MUT-22degrees_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 ("Gould_1-23_GI11-MUT-22degrees_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: Gould_1-23_GI11-MUT-22degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 22 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.367981
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.375015
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.594655
Spike_AFFX-r2-Bs-dap_5_signal4.260889
NoiseAvg:4.37,Std:0.09,Min:4.1,Max:4.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.331530
#P14495
Spike_AFFX-r2-Bs-phe_M_signal0.713262
Corner-Avg:12704,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal37.160957
Spike_AFFX-r2-Ec-bioB_3_signal21.593121
Spike_AFFX-r2-Bs-lys_M_signal0.352775
Spike_AFFX-r2-P1-cre_3_signal2361.352295
Spike_AFFX-r2-Bs-lys_3-5-ratio4.612449
Spike_AFFX-r2-Bs-dap_M_signal1.205315
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.054619
Spike_AFFX-r2-Ec-bioB_avg-signal31.688707
Spike_AFFX-r2-Bs-thr_avg-signal4.381642
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal323.945251
Spike_AFFX-r2-Bs-phe_5_signal2.500505
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal486.564697
RawQ2.915888
Spike_AFFX-r2-Bs-lys_5_signal0.126246
Signal(A)7.804970
%A33.954407
Signal(All)135.602844
Corner+Avg:130,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal105.981087
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal0.339077
Spike_AFFX-r2-Ec-bioD_avg-signal405.254974
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P63.546692
Spike_AFFX-r2-Bs-lys_avg-signal1.697157
Spike_AFFX-r2-P1-cre_avg-signal2039.340088
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.498904
Spike_AFFX-r2-Bs-thr_3_signal0.618913
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal1.184281
Spike_AFFX-r2-Bs-dap_3_signal0.456385
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.501997
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal105.775810
#M570
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal4.612449
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.001941
Spike_AFFX-r2-Bs-thr_M_signal1.194484
Signal(P)208.231415
Spike_AFFX-r2-Bs-phe_3-5-ratio0.135603
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:12028,Count:9
Spike_AFFX-r2-P1-cre_5_signal1717.327881
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7745
Signal(M)25.152697
BackgroundAvg:65.69,Std:0.97,Min:62.8,Max:67.8
Spike_AFFX-r2-Ec-bioC_avg-signal105.878448
Spike_AFFX-r2-Bs-dap_avg-signal1.974196
Spike_AFFX-r2-Bs-dap_3-5-ratio0.107110
Spike_AFFX-r2-Ec-bioB_5_signal36.312046
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.367981
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-24_GI11-MUT-27degrees_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 ("Gould_1-24_GI11-MUT-27degrees_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: Gould_1-24_GI11-MUT-27degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GI11 WS
Stock Code:
Genetic Background: WS
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 27 degrees for 3 to 4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.597305
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.310308
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.498101
Spike_AFFX-r2-Bs-dap_5_signal3.784262
NoiseAvg:3.42,Std:0.13,Min:3.2,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.187029
#P14236
Spike_AFFX-r2-Bs-phe_M_signal0.320891
Corner-Avg:12641,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal31.519823
Spike_AFFX-r2-Ec-bioB_3_signal33.260368
Spike_AFFX-r2-Bs-lys_M_signal2.622164
Spike_AFFX-r2-P1-cre_3_signal3341.843506
Spike_AFFX-r2-Bs-lys_3-5-ratio0.715433
Spike_AFFX-r2-Bs-dap_M_signal1.634819
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.130841
Spike_AFFX-r2-Ec-bioB_avg-signal43.851501
Spike_AFFX-r2-Bs-thr_avg-signal3.188643
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal449.138641
Spike_AFFX-r2-Bs-phe_5_signal5.852972
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal709.067444
RawQ2.451942
Spike_AFFX-r2-Bs-lys_5_signal2.177746
Signal(A)9.043735
%A35.076721
Signal(All)138.528519
Corner+Avg:124,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal155.718430
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal0.870016
Spike_AFFX-r2-Ec-bioD_avg-signal579.103027
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P62.411224
Spike_AFFX-r2-Bs-lys_avg-signal2.119314
Spike_AFFX-r2-P1-cre_avg-signal2946.134766
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.512056
Spike_AFFX-r2-Bs-thr_3_signal0.940357
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.347960
Spike_AFFX-r2-Bs-dap_3_signal0.247001
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.578727
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal152.480850
#M573
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal1.558032
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.021233
Spike_AFFX-r2-Bs-thr_M_signal1.438543
Signal(P)215.782974
Spike_AFFX-r2-Bs-phe_3-5-ratio0.148645
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10770,Count:9
Spike_AFFX-r2-P1-cre_5_signal2550.426025
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8001
Signal(M)27.207560
BackgroundAvg:58.82,Std:0.84,Min:57.2,Max:60.7
Spike_AFFX-r2-Ec-bioC_avg-signal154.099640
Spike_AFFX-r2-Bs-dap_avg-signal1.888694
Spike_AFFX-r2-Bs-dap_3-5-ratio0.065271
Spike_AFFX-r2-Ec-bioB_5_signal66.774323
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.597305
NF1.000000
HZ4
Tau0.015000

Hybridisation Set: Gould_Wild type

Slide: Gould_1-1_WT-WS-12degrees_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 ("Gould_1-1_WT-WS-12degrees_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: Gould_1-1_WT-WS-12degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.374815
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ3.91
NoiseAvg:5.93,Stdev:0.18,Max:6.4,Min:5.5
BackgroundAvg:105.42,Stdev:1.96,Max:109.4,Min:100.5
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.374815
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-2_WT-WS-17degrees_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 ("Gould_1-2_WT-WS-17degrees_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: Gould_1-2_WT-WS-17degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.324731
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ3.55
NoiseAvg:5.42,Stdev:0.18,Max:5.9,Min:5.0
BackgroundAvg:95.31,Stdev:1.43,Max:98.0,Min:91.8
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.324731
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-3_WT-WS-22degrees_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 ("Gould_1-3_WT-WS-22degrees_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: Gould_1-3_WT-WS-22degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.309359
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ4.76
NoiseAvg:7.45,Stdev:0.32,Max:8.8,Min:6.5
BackgroundAvg:139.89,Stdev:2.95,Max:145.6,Min:132.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.309359
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-4_WT-WS-27degrees_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 ("Gould_1-4_WT-WS-27degrees_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: Gould_1-4_WT-WS-27degrees_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Tissue: Cell culture
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.408527
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ3.53
NoiseAvg:5.19,Stdev:0.17,Max:5.6,Min:4.7
BackgroundAvg:95.17,Stdev:1.96,Max:99.7,Min:90.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.408527
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Gould_1-9_WT-WS-12degrees_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 ("Gould_1-9_WT-WS-12degrees_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: Gould_1-9_WT-WS-12degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 12C for 3 days harvesting on the third and fourth day
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.518434
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.383235
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.463564
Spike_AFFX-r2-Bs-dap_5_signal1.077508
NoiseAvg:5.34,Std:0.16,Min:4.9,Max:5.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal6.300604
#P13234
Spike_AFFX-r2-Bs-phe_M_signal1.053962
Corner-Avg:10308,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal24.797237
Spike_AFFX-r2-Ec-bioB_3_signal20.458105
Spike_AFFX-r2-Bs-lys_M_signal13.756562
Spike_AFFX-r2-P1-cre_3_signal2413.807129
Spike_AFFX-r2-Bs-lys_3-5-ratio6.067028
Spike_AFFX-r2-Bs-dap_M_signal1.662209
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.334189
Spike_AFFX-r2-Ec-bioB_avg-signal29.795855
Spike_AFFX-r2-Bs-thr_avg-signal3.241449
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal314.282318
Spike_AFFX-r2-Bs-phe_5_signal4.146586
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal491.410278
RawQ3.991025
Spike_AFFX-r2-Bs-lys_5_signal1.751686
Signal(A)10.018306
%A39.245945
Signal(All)143.975311
Corner+Avg:127,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal111.479652
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal1.770893
Spike_AFFX-r2-Ec-bioD_avg-signal402.846313
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P58.018414
Spike_AFFX-r2-Bs-lys_avg-signal8.711926
Spike_AFFX-r2-P1-cre_avg-signal2079.426025
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.735642
Spike_AFFX-r2-Bs-thr_3_signal2.105591
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.323814
Spike_AFFX-r2-Bs-dap_3_signal0.663266
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.563595
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal94.857986
#M624
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal10.627527
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.175227
Spike_AFFX-r2-Bs-thr_M_signal1.318153
Signal(P)239.896164
Spike_AFFX-r2-Bs-phe_3-5-ratio0.427073
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10117,Count:9
Spike_AFFX-r2-P1-cre_5_signal1745.044922
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8952
Signal(M)31.422026
BackgroundAvg:100.39,Std:1.43,Min:97.6,Max:103.7
Spike_AFFX-r2-Ec-bioC_avg-signal103.168823
Spike_AFFX-r2-Bs-dap_avg-signal1.134328
Spike_AFFX-r2-Bs-dap_3-5-ratio0.615555
Spike_AFFX-r2-Ec-bioB_5_signal44.132225
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.518434
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-10_WT-WS-17degrees_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 ("Gould_1-10_WT-WS-17degrees_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: Gould_1-10_WT-WS-17degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 17C for 3 days harvesting on the third and fourth day
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.62246
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.316688
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.955031
Spike_AFFX-r2-Bs-dap_5_signal0.760083
NoiseAvg:4.58,Std:0.26,Min:4.0,Max:6.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal4.840813
#P13634
Spike_AFFX-r2-Bs-phe_M_signal0.892789
Corner-Avg:8915,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal27.806044
Spike_AFFX-r2-Ec-bioB_3_signal27.310427
Spike_AFFX-r2-Bs-lys_M_signal0.343458
Spike_AFFX-r2-P1-cre_3_signal2429.504150
Spike_AFFX-r2-Bs-lys_3-5-ratio1.611865
Spike_AFFX-r2-Bs-dap_M_signal3.030591
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.134435
Spike_AFFX-r2-Ec-bioB_avg-signal27.904287
Spike_AFFX-r2-Bs-thr_avg-signal2.072504
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal280.442963
Spike_AFFX-r2-Bs-phe_5_signal0.698735
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal469.516479
RawQ3.678036
Spike_AFFX-r2-Bs-lys_5_signal1.873568
Signal(A)8.492409
%A38.066639
Signal(All)143.195251
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal93.462128
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal4.675994
Spike_AFFX-r2-Ec-bioD_avg-signal374.979736
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P59.772030
Spike_AFFX-r2-Bs-lys_avg-signal1.745654
Spike_AFFX-r2-P1-cre_avg-signal2137.333496
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.161333
Spike_AFFX-r2-Bs-thr_3_signal0.650775
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.089173
Spike_AFFX-r2-Bs-dap_3_signal0.814767
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.674196
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal96.910934
#M493
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal3.019938
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.964413
Spike_AFFX-r2-Bs-thr_M_signal0.725924
Signal(P)233.112289
Spike_AFFX-r2-Bs-phe_3-5-ratio4.675994
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:7539,Count:9
Spike_AFFX-r2-P1-cre_5_signal1845.163086
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8683
Signal(M)28.988319
BackgroundAvg:97.33,Std:1.60,Min:91.4,Max:100.7
Spike_AFFX-r2-Ec-bioC_avg-signal95.186531
Spike_AFFX-r2-Bs-dap_avg-signal1.535147
Spike_AFFX-r2-Bs-dap_3-5-ratio0.814767
Spike_AFFX-r2-Ec-bioB_5_signal28.596386
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.622460
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-11_WT-WS-22degrees_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 ("Gould_1-11_WT-WS-22degrees_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: Gould_1-11_WT-WS-22degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.676369726658
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
RawQ3.77
NoiseAvg:4.59,Stdev:0.15,Max:5.1,Min:4.2
Central-Avg:8949,Count:9
Corner+Avg:119,Count:32
Corner-Avg:10442,Count:32
BackgroundAvg:100.17,Stdev:2.19,Max:104.5,Min:94.6
Gamma1H0.0025
VZ4
Gamma2L0.003
Epsilon0.5
TGT100
Perturbation1.1
Alpha20.06
BF
BG4
Gamma2H0.003
SF0.676369726658
Alpha10.04
SFGeneAll
HZ4
NF1.000000000000
SmoothFactorBG100
Gamma1L0.0025
Tau0.015

Slide: Gould_1-12_WT-WS-27degrees_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 ("Gould_1-12_WT-WS-27degrees_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: Gould_1-12_WT-WS-27degrees_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 27 degrees for 3-4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.743805
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.284002
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.373138
Spike_AFFX-r2-Bs-dap_5_signal0.717490
NoiseAvg:4.34,Std:0.12,Min:3.9,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.025381
#P13936
Spike_AFFX-r2-Bs-phe_M_signal0.613713
Corner-Avg:9170,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal28.831249
Spike_AFFX-r2-Ec-bioB_3_signal19.371130
Spike_AFFX-r2-Bs-lys_M_signal0.210902
Spike_AFFX-r2-P1-cre_3_signal2773.590820
Spike_AFFX-r2-Bs-lys_3-5-ratio11.664027
Spike_AFFX-r2-Bs-dap_M_signal0.252577
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.213398
Spike_AFFX-r2-Ec-bioB_avg-signal33.372181
Spike_AFFX-r2-Bs-thr_avg-signal8.320180
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal374.806763
Spike_AFFX-r2-Bs-phe_5_signal0.268949
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal545.620544
RawQ3.598109
Spike_AFFX-r2-Bs-lys_5_signal0.940212
Signal(A)9.483005
%A36.444542
Signal(All)139.037033
Corner+Avg:97,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal134.532852
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal4.742834
Spike_AFFX-r2-Ec-bioD_avg-signal460.213654
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.096012
Spike_AFFX-r2-Bs-lys_avg-signal4.271714
Spike_AFFX-r2-P1-cre_avg-signal2466.852539
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.459448
Spike_AFFX-r2-Bs-thr_3_signal11.123167
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal1.875165
Spike_AFFX-r2-Bs-dap_3_signal0.812160
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.455738
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal118.380508
#M561
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal11.664027
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.136444
Spike_AFFX-r2-Bs-thr_M_signal8.811992
Signal(P)220.691666
Spike_AFFX-r2-Bs-phe_3-5-ratio4.742834
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:8042,Count:9
Spike_AFFX-r2-P1-cre_5_signal2160.114502
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8313
Signal(M)30.380842
BackgroundAvg:95.54,Std:2.05,Min:89.7,Max:99.8
Spike_AFFX-r2-Ec-bioC_avg-signal126.456680
Spike_AFFX-r2-Bs-dap_avg-signal0.594076
Spike_AFFX-r2-Bs-dap_3-5-ratio0.812160
Spike_AFFX-r2-Ec-bioB_5_signal51.914169
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.743805
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-13_WT-WS-12degrees_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 ("Gould_1-13_WT-WS-12degrees_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: Gould_1-13_WT-WS-12degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 12C for 3 days harvesting on the third and fourth day
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.486761
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.340486
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.711363
Spike_AFFX-r2-Bs-dap_5_signal0.863301
NoiseAvg:4.42,Std:0.16,Min:3.9,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.815031
#P13054
Spike_AFFX-r2-Bs-phe_M_signal6.683620
Corner-Avg:10789,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal37.020370
Spike_AFFX-r2-Ec-bioB_3_signal35.680641
Spike_AFFX-r2-Bs-lys_M_signal2.818115
Spike_AFFX-r2-P1-cre_3_signal2936.669189
Spike_AFFX-r2-Bs-lys_3-5-ratio6.949611
Spike_AFFX-r2-Bs-dap_M_signal0.471373
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.109679
Spike_AFFX-r2-Ec-bioB_avg-signal40.953060
Spike_AFFX-r2-Bs-thr_avg-signal4.682993
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal478.979767
Spike_AFFX-r2-Bs-phe_5_signal0.454963
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal740.883972
RawQ3.167533
Spike_AFFX-r2-Bs-lys_5_signal0.187913
Signal(A)10.426123
%A39.785183
Signal(All)146.548264
Corner+Avg:123,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal149.991776
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal3.543298
Spike_AFFX-r2-Ec-bioD_avg-signal609.931885
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P57.229286
Spike_AFFX-r2-Bs-lys_avg-signal3.318546
Spike_AFFX-r2-P1-cre_avg-signal2563.709473
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.985533
Spike_AFFX-r2-Bs-thr_3_signal1.076507
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal3.560628
Spike_AFFX-r2-Bs-dap_3_signal0.362301
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.546796
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal146.963211
#M681
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal6.949611
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.020608
Spike_AFFX-r2-Bs-thr_M_signal3.157443
Signal(P)247.180344
Spike_AFFX-r2-Bs-phe_3-5-ratio3.543298
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:12495,Count:9
Spike_AFFX-r2-P1-cre_5_signal2190.749512
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9075
Signal(M)31.507555
BackgroundAvg:77.15,Std:1.07,Min:74.3,Max:79.6
Spike_AFFX-r2-Ec-bioC_avg-signal148.477493
Spike_AFFX-r2-Bs-dap_avg-signal0.565659
Spike_AFFX-r2-Bs-dap_3-5-ratio0.362301
Spike_AFFX-r2-Ec-bioB_5_signal50.158165
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.486761
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-14_WT-WS-17degrees_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 ("Gould_1-14_WT-WS-17degrees_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: Gould_1-14_WT-WS-17degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 17C for 3 days harvesting on the third and fourth day
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.38912
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.480688
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.573864
Spike_AFFX-r2-Bs-dap_5_signal0.278153
NoiseAvg:4.52,Std:0.13,Min:4.1,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.048414
#P14178
Spike_AFFX-r2-Bs-phe_M_signal0.737173
Corner-Avg:12267,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal19.163450
Spike_AFFX-r2-Ec-bioB_3_signal23.661980
Spike_AFFX-r2-Bs-lys_M_signal4.047708
Spike_AFFX-r2-P1-cre_3_signal2322.631104
Spike_AFFX-r2-Bs-lys_3-5-ratio1.676834
Spike_AFFX-r2-Bs-dap_M_signal0.417710
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.043862
Spike_AFFX-r2-Ec-bioB_avg-signal28.019388
Spike_AFFX-r2-Bs-thr_avg-signal4.144212
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal285.163116
Spike_AFFX-r2-Bs-phe_5_signal0.418259
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal408.066315
RawQ3.298812
Spike_AFFX-r2-Bs-lys_5_signal2.547146
Signal(A)7.260693
%A35.322227
Signal(All)139.926788
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal89.934174
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal1.035516
Spike_AFFX-r2-Ec-bioD_avg-signal346.614716
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P62.156948
Spike_AFFX-r2-Bs-lys_avg-signal3.621999
Spike_AFFX-r2-P1-cre_avg-signal1945.623413
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.520824
Spike_AFFX-r2-Bs-thr_3_signal0.484603
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal0.730316
Spike_AFFX-r2-Bs-dap_3_signal0.787251
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.430993
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal85.415314
#M575
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal4.271142
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.052905
Spike_AFFX-r2-Bs-thr_M_signal0.899620
Signal(P)220.056091
Spike_AFFX-r2-Bs-phe_3-5-ratio1.035516
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:11484,Count:9
Spike_AFFX-r2-P1-cre_5_signal1568.615723
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8057
Signal(M)23.087353
BackgroundAvg:83.57,Std:1.77,Min:77.4,Max:86.6
Spike_AFFX-r2-Ec-bioC_avg-signal87.674744
Spike_AFFX-r2-Bs-dap_avg-signal0.494371
Spike_AFFX-r2-Bs-dap_3-5-ratio0.787251
Spike_AFFX-r2-Ec-bioB_5_signal41.232738
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.389120
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-15_WT-WS-22degrees_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 ("Gould_1-15_WT-WS-22degrees_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: Gould_1-15_WT-WS-22degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Treatmentnone
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.443047
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.544163
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.616475
Spike_AFFX-r2-Bs-dap_5_signal0.808908
NoiseAvg:4.34,Std:0.17,Min:3.6,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal0.826540
#P14018
Spike_AFFX-r2-Bs-phe_M_signal0.726426
Corner-Avg:10303,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal33.450294
Spike_AFFX-r2-Ec-bioB_3_signal28.679508
Spike_AFFX-r2-Bs-lys_M_signal4.860467
Spike_AFFX-r2-P1-cre_3_signal2826.135010
Spike_AFFX-r2-Bs-lys_3-5-ratio3.763375
Spike_AFFX-r2-Bs-dap_M_signal0.218233
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.792417
Spike_AFFX-r2-Ec-bioB_avg-signal36.217194
Spike_AFFX-r2-Bs-thr_avg-signal1.320611
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal348.306763
Spike_AFFX-r2-Bs-phe_5_signal8.614252
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal538.664063
RawQ3.100811
Spike_AFFX-r2-Bs-lys_5_signal1.056100
Signal(A)8.417099
%A36.019291
Signal(All)140.991302
Corner+Avg:119,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal102.878838
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal5.991043
Spike_AFFX-r2-Ec-bioD_avg-signal443.485413
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.455502
Spike_AFFX-r2-Bs-lys_avg-signal3.297023
Spike_AFFX-r2-P1-cre_avg-signal2328.169922
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.525208
Spike_AFFX-r2-Bs-thr_3_signal1.792417
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal5.110574
Spike_AFFX-r2-Bs-dap_3_signal0.283612
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.546522
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal109.122391
#M576
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal3.974502
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.942784
Spike_AFFX-r2-Bs-thr_M_signal1.342877
Signal(P)223.328369
Spike_AFFX-r2-Bs-phe_3-5-ratio0.695480
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:11435,Count:9
Spike_AFFX-r2-P1-cre_5_signal1830.204834
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8216
Signal(M)28.193966
BackgroundAvg:72.54,Std:1.46,Min:68.3,Max:75.1
Spike_AFFX-r2-Ec-bioC_avg-signal106.000610
Spike_AFFX-r2-Bs-dap_avg-signal0.436918
Spike_AFFX-r2-Bs-dap_3-5-ratio0.283612
Spike_AFFX-r2-Ec-bioB_5_signal46.521778
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.443047
NF1.000000
HZ4
Tau0.015000

Slide: Gould_1-16_WT-WS-27degrees_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 ("Gould_1-16_WT-WS-27degrees_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: Gould_1-16_WT-WS-27degrees_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: WS
Stock Code:
Growth Conditions:
locationtemp and light controlled incubators
AtmosphereNormal
Humiditynormal
Temperature22C for 7 days followed by 27 degrees for 3-4 days
Lighting(Source: saturation)for 7 days 22C 12hours light and 12 hours dark then transferred to constant light
Medium2.5% agar murashige and Skoog
Nutrients3% sucrose
Stratificationonce seeds sterilised upon plating out placed at 4C for 2 days
Developmental Stage:
Growth Stageseedlings
Tissue: whole seedling
Diseased: Normal
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen RNAeasy kit
Method:
ProtocolSeedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.517407
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:
Spike_AFFX-r2-P1-cre_3-5-ratio1.465158
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.730224
Spike_AFFX-r2-Bs-dap_5_signal0.385520
NoiseAvg:3.68,Std:0.13,Min:3.3,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.479061
#P14516
Spike_AFFX-r2-Bs-phe_M_signal2.154958
Corner-Avg:9659,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal35.255623
Spike_AFFX-r2-Ec-bioB_3_signal28.055794
Spike_AFFX-r2-Bs-lys_M_signal6.635089
Spike_AFFX-r2-P1-cre_3_signal2771.066895
Spike_AFFX-r2-Bs-lys_3-5-ratio5.376043
Spike_AFFX-r2-Bs-dap_M_signal0.219908
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.317117
Spike_AFFX-r2-Ec-bioB_avg-signal33.910748
Spike_AFFX-r2-Bs-thr_avg-signal1.212029
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal373.441315
Spike_AFFX-r2-Bs-phe_5_signal0.232745
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal627.192993
RawQ2.759430
Spike_AFFX-r2-Bs-lys_5_signal0.536181
Signal(A)7.510393
%A33.980709
Signal(All)138.691406
Corner+Avg:109,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal111.450157
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal1.213589
Spike_AFFX-r2-Ec-bioD_avg-signal500.317139
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P63.638756
Spike_AFFX-r2-Bs-lys_avg-signal4.182437
Spike_AFFX-r2-P1-cre_avg-signal2331.187744
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.380535
Spike_AFFX-r2-Bs-thr_3_signal0.786151
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal1.200431
Spike_AFFX-r2-Bs-dap_3_signal0.576077
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.679495
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal129.158783
#M543
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal5.376043
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.862893
Spike_AFFX-r2-Bs-thr_M_signal0.370874
Signal(P)213.044479
Spike_AFFX-r2-Bs-phe_3-5-ratio1.213589
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:10340,Count:9
Spike_AFFX-r2-P1-cre_5_signal1891.308594
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7751
Signal(M)23.543753
BackgroundAvg:68.61,Std:1.05,Min:64.7,Max:71.0
Spike_AFFX-r2-Ec-bioC_avg-signal120.304474
Spike_AFFX-r2-Bs-dap_avg-signal0.393835
Spike_AFFX-r2-Bs-dap_3-5-ratio0.576077
Spike_AFFX-r2-Ec-bioB_5_signal38.420818
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.517407
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team