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Experiment: Calcium and the clock

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-529

We are aiming to analyze calcium effect on the circadian clock. Untrained plants lacking a calcium rhythm and artificially restored rhythm via ectopic calcium pulse. Plants were grown 10days in continuous light and then subjected to calcium/water treatment. Ramping from the subjective dawn: 0.5, 1, 5, 10, 20, 50, 60 mM CaCl2 for an hour. Every point (sampling every 4h) made in duplicate, with a water treated control. WT col used.

About the Experimenter

Name:Dr Sylvain Aubry
Head of Lab Name: Julian Hibberd
Lab:
Address:Department of Plant Sciences, University of Cambridge
Downing street, Cambridge, Cambridgeshire, CB2 3EA, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 0122330220

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:28
 
Experimental Parameters:
parameter compound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Aubry: Calcium and the clock

Slide: Aubry_1-1_Water_0h_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Aubry_1-1_Water_0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-1_Water_0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.516304
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-ratio1.375385
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.209376
Spike_AFFX-r2-Bs-dap_5_signal50.533596
NoiseAvg:3.28,Std:0.34,Min:2.8,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_signal27.772726
#P15520
Spike_AFFX-r2-Bs-phe_M_signal25.324562
Corner-Avg:14636,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.903862
Spike_AFFX-r2-Ec-bioB_3_signal85.971542
Spike_AFFX-r2-Bs-lys_M_signal14.225053
Spike_AFFX-r2-P1-cre_3_signal4902.525879
Spike_AFFX-r2-Bs-lys_3-5-ratio2.962298
Spike_AFFX-r2-Bs-dap_M_signal177.572464
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.480862
Spike_AFFX-r2-Ec-bioB_avg-signal82.987648
Spike_AFFX-r2-Bs-thr_avg-signal71.617088
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1080.196899
Spike_AFFX-r2-Bs-phe_5_signal19.983404
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1420.839844
RawQ2.655299
Spike_AFFX-r2-Bs-lys_5_signal17.980770
Signal(A)4.012511
%A30.416485
Signal(All)139.179382
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal288.817017
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal67.276878
Spike_AFFX-r2-Ec-bioD_avg-signal1250.518311
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.040337
Spike_AFFX-r2-Bs-lys_avg-signal28.490072
Spike_AFFX-r2-P1-cre_avg-signal4233.500977
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.543183
Spike_AFFX-r2-Bs-thr_3_signal124.445763
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal37.528282
Spike_AFFX-r2-Bs-dap_3_signal304.571045
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.315353
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal260.687927
#M352
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.264393
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.107903
Spike_AFFX-r2-Bs-thr_M_signal62.632786
Signal(P)202.428299
Spike_AFFX-r2-Bs-phe_3-5-ratio3.366637
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10489,Count:9
Spike_AFFX-r2-P1-cre_5_signal3564.476563
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6938
Signal(M)14.646606
BackgroundAvg:65.11,Std:0.92,Min:62.7,Max:67.3
Spike_AFFX-r2-Ec-bioC_avg-signal274.752472
Spike_AFFX-r2-Bs-dap_avg-signal177.559021
Spike_AFFX-r2-Bs-dap_3-5-ratio6.027100
Spike_AFFX-r2-Ec-bioB_5_signal71.087540
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.516304
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-2_Water_0h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-2_Water_0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-2_Water_0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.233706
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-ratio1.269590
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.100349
Spike_AFFX-r2-Bs-dap_5_signal155.575943
NoiseAvg:2.39,Std:0.08,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal56.424969
#P14418
Spike_AFFX-r2-Bs-phe_M_signal93.027985
Corner-Avg:10628,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal207.150345
Spike_AFFX-r2-Ec-bioB_3_signal185.194778
Spike_AFFX-r2-Bs-lys_M_signal50.696819
Spike_AFFX-r2-P1-cre_3_signal10454.938477
Spike_AFFX-r2-Bs-lys_3-5-ratio2.406438
Spike_AFFX-r2-Bs-dap_M_signal456.660950
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.009196
Spike_AFFX-r2-Ec-bioB_avg-signal186.883530
Spike_AFFX-r2-Bs-thr_avg-signal238.120300
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2354.492188
Spike_AFFX-r2-Bs-phe_5_signal74.587456
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal3348.425781
RawQ2.324600
Spike_AFFX-r2-Bs-lys_5_signal35.362644
Signal(A)7.077693
%A34.765453
Signal(All)147.867676
Corner+Avg:99,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal737.145752
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal159.500473
Spike_AFFX-r2-Ec-bioD_avg-signal2851.458984
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.209118
Spike_AFFX-r2-Bs-lys_avg-signal57.052486
Spike_AFFX-r2-P1-cre_avg-signal9344.916992
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.025427
Spike_AFFX-r2-Bs-thr_3_signal451.918640
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal109.038635
Spike_AFFX-r2-Bs-dap_3_signal843.466431
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.422143
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal651.563843
#M462
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal85.098000
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.131348
Spike_AFFX-r2-Bs-thr_M_signal206.017242
Signal(P)229.231262
Spike_AFFX-r2-Bs-phe_3-5-ratio2.138436
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7625,Count:9
Spike_AFFX-r2-P1-cre_5_signal8234.895508
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7930
Signal(M)25.279572
BackgroundAvg:58.13,Std:0.80,Min:56.7,Max:60.7
Spike_AFFX-r2-Ec-bioC_avg-signal694.354797
Spike_AFFX-r2-Bs-dap_avg-signal485.234467
Spike_AFFX-r2-Bs-dap_3-5-ratio5.421574
Spike_AFFX-r2-Ec-bioB_5_signal168.305450
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.233706
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-3_Water_4h_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 ("Aubry_1-3_Water_4h_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: Aubry_1-3_Water_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.604451
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-ratio1.267218
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.063933
Spike_AFFX-r2-Bs-dap_5_signal53.455448
NoiseAvg:2.77,Std:0.07,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.753008
#P15483
Spike_AFFX-r2-Bs-phe_M_signal30.082373
Corner-Avg:11301,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.444870
Spike_AFFX-r2-Ec-bioB_3_signal68.071388
Spike_AFFX-r2-Bs-lys_M_signal12.575208
Spike_AFFX-r2-P1-cre_3_signal4412.742188
Spike_AFFX-r2-Bs-lys_3-5-ratio2.764497
Spike_AFFX-r2-Bs-dap_M_signal220.169296
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.289983
Spike_AFFX-r2-Ec-bioB_avg-signal72.832390
Spike_AFFX-r2-Bs-thr_avg-signal80.185593
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal799.569946
Spike_AFFX-r2-Bs-phe_5_signal31.398319
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1357.760864
RawQ2.553247
Spike_AFFX-r2-Bs-lys_5_signal15.201039
Signal(A)3.950649
%A30.512934
Signal(All)137.710953
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.852249
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal57.130184
Spike_AFFX-r2-Ec-bioD_avg-signal1078.665405
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.878120
Spike_AFFX-r2-Bs-lys_avg-signal23.266489
Spike_AFFX-r2-P1-cre_avg-signal3947.485596
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal155.635147
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal39.536957
Spike_AFFX-r2-Bs-dap_3_signal327.313904
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.698114
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal214.309204
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.023220
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.193846
Spike_AFFX-r2-Bs-thr_M_signal68.168625
Signal(P)200.762253
Spike_AFFX-r2-Bs-phe_3-5-ratio1.819530
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8018,Count:9
Spike_AFFX-r2-P1-cre_5_signal3482.229004
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6960
Signal(M)14.409853
BackgroundAvg:62.66,Std:0.58,Min:61.2,Max:64.2
Spike_AFFX-r2-Ec-bioC_avg-signal235.080719
Spike_AFFX-r2-Bs-dap_avg-signal200.312881
Spike_AFFX-r2-Bs-dap_3-5-ratio6.123116
Spike_AFFX-r2-Ec-bioB_5_signal63.980911
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.604451
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-4_Water_4h_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 ("Aubry_1-4_Water_4h_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: Aubry_1-4_Water_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.047544
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-ratio1.337923
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.245400
Spike_AFFX-r2-Bs-dap_5_signal220.488449
NoiseAvg:2.70,Std:0.08,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal75.041939
#P14610
Spike_AFFX-r2-Bs-phe_M_signal87.590355
Corner-Avg:17454,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal215.894302
Spike_AFFX-r2-Ec-bioB_3_signal179.932632
Spike_AFFX-r2-Bs-lys_M_signal55.428986
Spike_AFFX-r2-P1-cre_3_signal9160.568359
Spike_AFFX-r2-Bs-lys_3-5-ratio1.554475
Spike_AFFX-r2-Bs-dap_M_signal507.519653
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.352459
Spike_AFFX-r2-Ec-bioB_avg-signal180.101563
Spike_AFFX-r2-Bs-thr_avg-signal231.069809
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2043.880493
Spike_AFFX-r2-Bs-phe_5_signal70.586823
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2959.947266
RawQ2.604680
Spike_AFFX-r2-Bs-lys_5_signal53.456200
Signal(A)6.201788
%A34.156071
Signal(All)143.560623
Corner+Avg:155,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal578.613586
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal161.379913
Spike_AFFX-r2-Ec-bioD_avg-signal2501.913818
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.050858
Spike_AFFX-r2-Bs-lys_avg-signal63.993835
Spike_AFFX-r2-P1-cre_avg-signal8003.712891
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.793073
Spike_AFFX-r2-Bs-thr_3_signal401.658905
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal106.519035
Spike_AFFX-r2-Bs-dap_3_signal893.723755
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.448200
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal488.300446
#M409
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal83.096321
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.184954
Spike_AFFX-r2-Bs-thr_M_signal216.508560
Signal(P)220.231964
Spike_AFFX-r2-Bs-phe_3-5-ratio2.286261
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14432,Count:9
Spike_AFFX-r2-P1-cre_5_signal6846.856934
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7791
Signal(M)21.297924
BackgroundAvg:67.98,Std:0.68,Min:66.2,Max:69.7
Spike_AFFX-r2-Ec-bioC_avg-signal533.457031
Spike_AFFX-r2-Bs-dap_avg-signal540.577271
Spike_AFFX-r2-Bs-dap_3-5-ratio4.053381
Spike_AFFX-r2-Ec-bioB_5_signal144.477768
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.047544
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-5_Water_8h_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 ("Aubry_1-5_Water_8h_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: Aubry_1-5_Water_8h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.651753
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-ratio1.343653
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.374716
Spike_AFFX-r2-Bs-dap_5_signal117.419029
NoiseAvg:3.07,Std:0.12,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal33.362888
#P15505
Spike_AFFX-r2-Bs-phe_M_signal58.709572
Corner-Avg:19660,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal133.105148
Spike_AFFX-r2-Ec-bioB_3_signal122.656044
Spike_AFFX-r2-Bs-lys_M_signal31.924885
Spike_AFFX-r2-P1-cre_3_signal6089.026855
Spike_AFFX-r2-Bs-lys_3-5-ratio2.116042
Spike_AFFX-r2-Bs-dap_M_signal321.156464
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.662876
Spike_AFFX-r2-Ec-bioB_avg-signal114.994667
Spike_AFFX-r2-Bs-thr_avg-signal119.868217
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1334.486450
Spike_AFFX-r2-Bs-phe_5_signal52.237617
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1902.153076
RawQ2.751844
Spike_AFFX-r2-Bs-lys_5_signal32.275070
Signal(A)4.457621
%A30.548006
Signal(All)140.173553
Corner+Avg:172,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal394.543060
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal112.852036
Spike_AFFX-r2-Ec-bioD_avg-signal1618.319824
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.974571
Spike_AFFX-r2-Bs-lys_avg-signal44.165127
Spike_AFFX-r2-P1-cre_avg-signal5310.361328
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.477422
Spike_AFFX-r2-Bs-thr_3_signal222.292786
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal74.599739
Spike_AFFX-r2-Bs-dap_3_signal609.890503
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.425382
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal326.188904
#M337
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal68.295418
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.209554
Spike_AFFX-r2-Bs-thr_M_signal103.948967
Signal(P)203.846909
Spike_AFFX-r2-Bs-phe_3-5-ratio2.160360
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16196,Count:9
Spike_AFFX-r2-P1-cre_5_signal4531.695313
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6968
Signal(M)16.770512
BackgroundAvg:72.01,Std:0.52,Min:70.0,Max:72.9
Spike_AFFX-r2-Ec-bioC_avg-signal360.365967
Spike_AFFX-r2-Bs-dap_avg-signal349.488678
Spike_AFFX-r2-Bs-dap_3-5-ratio5.194137
Spike_AFFX-r2-Ec-bioB_5_signal89.222816
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.651753
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-6_Water_8h_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 ("Aubry_1-6_Water_8h_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: Aubry_1-6_Water_8h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.623772
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-ratio1.138545
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.933228
Spike_AFFX-r2-Bs-dap_5_signal76.678856
NoiseAvg:2.67,Std:0.12,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.855343
#P15417
Spike_AFFX-r2-Bs-phe_M_signal35.980587
Corner-Avg:12020,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.787804
Spike_AFFX-r2-Ec-bioB_3_signal66.927925
Spike_AFFX-r2-Bs-lys_M_signal18.336363
Spike_AFFX-r2-P1-cre_3_signal4281.934082
Spike_AFFX-r2-Bs-lys_3-5-ratio2.269648
Spike_AFFX-r2-Bs-dap_M_signal272.992249
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.788584
Spike_AFFX-r2-Ec-bioB_avg-signal77.144096
Spike_AFFX-r2-Bs-thr_avg-signal113.351158
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal847.748352
Spike_AFFX-r2-Bs-phe_5_signal37.674412
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1277.431030
RawQ2.381035
Spike_AFFX-r2-Bs-lys_5_signal20.441374
Signal(A)4.187216
%A30.868040
Signal(All)138.968552
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal277.399017
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal79.676582
Spike_AFFX-r2-Ec-bioD_avg-signal1062.589722
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.588776
Spike_AFFX-r2-Bs-lys_avg-signal28.390818
Spike_AFFX-r2-P1-cre_avg-signal4021.408691
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.543183
Spike_AFFX-r2-Bs-thr_3_signal224.999619
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal51.110523
Spike_AFFX-r2-Bs-dap_3_signal456.773346
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.506852
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal230.609604
#M352
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.394714
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.202894
Spike_AFFX-r2-Bs-thr_M_signal94.198517
Signal(P)203.342804
Spike_AFFX-r2-Bs-phe_3-5-ratio2.114873
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8115,Count:9
Spike_AFFX-r2-P1-cre_5_signal3760.883301
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7041
Signal(M)15.495965
BackgroundAvg:61.47,Std:0.65,Min:59.7,Max:62.8
Spike_AFFX-r2-Ec-bioC_avg-signal254.004303
Spike_AFFX-r2-Bs-dap_avg-signal268.814819
Spike_AFFX-r2-Bs-dap_3-5-ratio5.956966
Spike_AFFX-r2-Ec-bioB_5_signal71.716545
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.623772
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-7_Water_12h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-7_Water_12h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-7_Water_12h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.53688
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-ratio1.348515
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.357118
Spike_AFFX-r2-Bs-dap_5_signal88.333389
NoiseAvg:3.21,Std:0.12,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.696722
#P15104
Spike_AFFX-r2-Bs-phe_M_signal45.408451
Corner-Avg:19433,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.529541
Spike_AFFX-r2-Ec-bioB_3_signal83.115623
Spike_AFFX-r2-Bs-lys_M_signal34.519051
Spike_AFFX-r2-P1-cre_3_signal4478.484863
Spike_AFFX-r2-Bs-lys_3-5-ratio2.860529
Spike_AFFX-r2-Bs-dap_M_signal255.044205
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.650970
Spike_AFFX-r2-Ec-bioB_avg-signal80.296463
Spike_AFFX-r2-Bs-thr_avg-signal107.140984
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal861.160034
Spike_AFFX-r2-Bs-phe_5_signal39.061764
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1244.187378
RawQ2.714820
Spike_AFFX-r2-Bs-lys_5_signal21.603420
Signal(A)4.264384
%A32.327927
Signal(All)138.245468
Corner+Avg:209,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal241.283493
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal96.854401
Spike_AFFX-r2-Ec-bioD_avg-signal1052.673706
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.216568
Spike_AFFX-r2-Bs-lys_avg-signal39.306564
Spike_AFFX-r2-P1-cre_avg-signal3899.767090
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.455502
Spike_AFFX-r2-Bs-thr_3_signal197.512024
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal60.441540
Spike_AFFX-r2-Bs-dap_3_signal489.550385
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.444781
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal198.235611
#M332
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.797215
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.217155
Spike_AFFX-r2-Bs-thr_M_signal94.214195
Signal(P)206.351440
Spike_AFFX-r2-Bs-phe_3-5-ratio2.479519
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15454,Count:9
Spike_AFFX-r2-P1-cre_5_signal3321.049072
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7374
Signal(M)15.667068
BackgroundAvg:73.04,Std:0.54,Min:71.4,Max:74.3
Spike_AFFX-r2-Ec-bioC_avg-signal219.759552
Spike_AFFX-r2-Bs-dap_avg-signal277.642670
Spike_AFFX-r2-Bs-dap_3-5-ratio5.542076
Spike_AFFX-r2-Ec-bioB_5_signal61.244221
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.536880
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-8_Water_12h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-8_Water_12h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-8_Water_12h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.633715
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-ratio1.508224
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.249992
Spike_AFFX-r2-Bs-dap_5_signal79.327507
NoiseAvg:3.06,Std:0.10,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.913837
#P15391
Spike_AFFX-r2-Bs-phe_M_signal34.637257
Corner-Avg:16623,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.578606
Spike_AFFX-r2-Ec-bioB_3_signal63.089054
Spike_AFFX-r2-Bs-lys_M_signal15.939433
Spike_AFFX-r2-P1-cre_3_signal4197.569824
Spike_AFFX-r2-Bs-lys_3-5-ratio1.766516
Spike_AFFX-r2-Bs-dap_M_signal164.528671
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.619582
Spike_AFFX-r2-Ec-bioB_avg-signal66.046417
Spike_AFFX-r2-Bs-thr_avg-signal65.080505
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal789.895020
Spike_AFFX-r2-Bs-phe_5_signal20.783123
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1160.177002
RawQ2.612675
Spike_AFFX-r2-Bs-lys_5_signal18.702761
Signal(A)4.598669
%A30.925034
Signal(All)138.829239
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal200.245926
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal70.564598
Spike_AFFX-r2-Ec-bioD_avg-signal975.036011
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.474792
Spike_AFFX-r2-Bs-lys_avg-signal22.560305
Spike_AFFX-r2-P1-cre_avg-signal3490.345215
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal119.711090
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal41.994995
Spike_AFFX-r2-Bs-dap_3_signal243.550613
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.468774
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal198.680710
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.038723
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.007878
Spike_AFFX-r2-Bs-thr_M_signal49.616589
Signal(P)203.247894
Spike_AFFX-r2-Bs-phe_3-5-ratio3.395284
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13433,Count:9
Spike_AFFX-r2-P1-cre_5_signal2783.120850
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7054
Signal(M)16.624090
BackgroundAvg:70.42,Std:0.67,Min:69.2,Max:72.0
Spike_AFFX-r2-Ec-bioC_avg-signal199.463318
Spike_AFFX-r2-Bs-dap_avg-signal162.468933
Spike_AFFX-r2-Bs-dap_3-5-ratio3.070191
Spike_AFFX-r2-Ec-bioB_5_signal50.471581
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.633715
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-9_Water_16h_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 ("Aubry_1-9_Water_16h_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: Aubry_1-9_Water_16h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.940258
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-ratio1.349820
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.004807
Spike_AFFX-r2-Bs-dap_5_signal63.621788
NoiseAvg:2.28,Std:0.13,Min:2.0,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal37.373550
#P14893
Spike_AFFX-r2-Bs-phe_M_signal34.906944
Corner-Avg:10773,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal126.711205
Spike_AFFX-r2-Ec-bioB_3_signal103.372643
Spike_AFFX-r2-Bs-lys_M_signal24.179449
Spike_AFFX-r2-P1-cre_3_signal6135.417969
Spike_AFFX-r2-Bs-lys_3-5-ratio2.269876
Spike_AFFX-r2-Bs-dap_M_signal238.870529
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.822398
Spike_AFFX-r2-Ec-bioB_avg-signal110.987328
Spike_AFFX-r2-Bs-thr_avg-signal128.406845
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1225.212158
Spike_AFFX-r2-Bs-phe_5_signal27.943764
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1704.134399
RawQ2.229280
Spike_AFFX-r2-Bs-lys_5_signal20.494089
Signal(A)5.219065
%A33.051292
Signal(All)142.005600
Corner+Avg:96,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal374.657379
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal63.621872
Spike_AFFX-r2-Ec-bioD_avg-signal1464.673340
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.291542
Spike_AFFX-r2-Bs-lys_avg-signal30.397524
Spike_AFFX-r2-P1-cre_avg-signal5340.389160
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.657168
Spike_AFFX-r2-Bs-thr_3_signal254.977249
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal42.157528
Spike_AFFX-r2-Bs-dap_3_signal462.305969
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.390889
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal313.916321
#M378
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.519035
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.193494
Spike_AFFX-r2-Bs-thr_M_signal92.869713
Signal(P)214.352005
Spike_AFFX-r2-Bs-phe_3-5-ratio2.276783
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7128,Count:9
Spike_AFFX-r2-P1-cre_5_signal4545.360352
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7539
Signal(M)19.727100
BackgroundAvg:77.82,Std:1.89,Min:73.0,Max:81.2
Spike_AFFX-r2-Ec-bioC_avg-signal344.286865
Spike_AFFX-r2-Bs-dap_avg-signal254.932755
Spike_AFFX-r2-Bs-dap_3-5-ratio7.266472
Spike_AFFX-r2-Ec-bioB_5_signal102.878143
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.940258
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-10_Water_16h_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 ("Aubry_1-10_Water_16h_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: Aubry_1-10_Water_16h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.796207
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-ratio1.365747
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.862646
Spike_AFFX-r2-Bs-dap_5_signal87.194931
NoiseAvg:2.59,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.145836
#P15318
Spike_AFFX-r2-Bs-phe_M_signal49.975349
Corner-Avg:16036,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal109.801102
Spike_AFFX-r2-Ec-bioB_3_signal104.487564
Spike_AFFX-r2-Bs-lys_M_signal24.602345
Spike_AFFX-r2-P1-cre_3_signal5285.157715
Spike_AFFX-r2-Bs-lys_3-5-ratio1.861678
Spike_AFFX-r2-Bs-dap_M_signal253.902405
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.075407
Spike_AFFX-r2-Ec-bioB_avg-signal90.128319
Spike_AFFX-r2-Bs-thr_avg-signal106.466118
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal952.084473
Spike_AFFX-r2-Bs-phe_5_signal31.590748
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1442.364746
RawQ2.387177
Spike_AFFX-r2-Bs-lys_5_signal25.790258
Signal(A)4.914499
%A31.332748
Signal(All)138.353745
Corner+Avg:129,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal295.514526
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal91.246025
Spike_AFFX-r2-Ec-bioD_avg-signal1197.224609
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.154755
Spike_AFFX-r2-Bs-lys_avg-signal32.801922
Spike_AFFX-r2-P1-cre_avg-signal4577.475586
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal219.133286
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal57.604038
Spike_AFFX-r2-Bs-dap_3_signal380.297729
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.514955
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal244.915558
#M345
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.013157
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.206598
Spike_AFFX-r2-Bs-thr_M_signal76.119202
Signal(P)203.316101
Spike_AFFX-r2-Bs-phe_3-5-ratio2.888378
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13636,Count:9
Spike_AFFX-r2-P1-cre_5_signal3869.793457
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7147
Signal(M)18.344448
BackgroundAvg:81.81,Std:0.61,Min:80.5,Max:83.3
Spike_AFFX-r2-Ec-bioC_avg-signal270.215027
Spike_AFFX-r2-Bs-dap_avg-signal240.465027
Spike_AFFX-r2-Bs-dap_3-5-ratio4.361466
Spike_AFFX-r2-Ec-bioB_5_signal56.096298
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.796207
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-11_Water_20h_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 ("Aubry_1-11_Water_20h_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: Aubry_1-11_Water_20h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.633014
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-ratio1.116143
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.624357
Spike_AFFX-r2-Bs-dap_5_signal54.565895
NoiseAvg:2.85,Std:0.14,Min:2.5,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.650114
#P15068
Spike_AFFX-r2-Bs-phe_M_signal25.051283
Corner-Avg:15245,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.538483
Spike_AFFX-r2-Ec-bioB_3_signal72.908546
Spike_AFFX-r2-Bs-lys_M_signal12.224245
Spike_AFFX-r2-P1-cre_3_signal3447.275146
Spike_AFFX-r2-Bs-lys_3-5-ratio2.076133
Spike_AFFX-r2-Bs-dap_M_signal141.201599
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.740067
Spike_AFFX-r2-Ec-bioB_avg-signal64.110527
Spike_AFFX-r2-Bs-thr_avg-signal63.490063
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal655.931763
Spike_AFFX-r2-Bs-phe_5_signal18.701059
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1080.380005
RawQ2.559096
Spike_AFFX-r2-Bs-lys_5_signal18.216434
Signal(A)4.579385
%A32.235863
Signal(All)136.720734
Corner+Avg:137,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.715363
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.316681
Spike_AFFX-r2-Ec-bioD_avg-signal868.155884
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.058746
Spike_AFFX-r2-Bs-lys_avg-signal22.753479
Spike_AFFX-r2-P1-cre_avg-signal3267.916992
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal112.103111
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal35.023006
Spike_AFFX-r2-Bs-dap_3_signal266.258484
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.647092
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.277664
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.819752
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.364004
Spike_AFFX-r2-Bs-thr_M_signal54.716949
Signal(P)204.286469
Spike_AFFX-r2-Bs-phe_3-5-ratio3.278781
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13122,Count:9
Spike_AFFX-r2-P1-cre_5_signal3088.559082
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7353
Signal(M)17.324806
BackgroundAvg:88.08,Std:0.71,Min:86.1,Max:89.6
Spike_AFFX-r2-Ec-bioC_avg-signal205.996521
Spike_AFFX-r2-Bs-dap_avg-signal154.008652
Spike_AFFX-r2-Bs-dap_3-5-ratio4.879577
Spike_AFFX-r2-Ec-bioB_5_signal44.884544
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.633014
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-12_Water_20h_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 ("Aubry_1-12_Water_20h_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: Aubry_1-12_Water_20h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.659571
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-ratio1.287155
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.785901
Spike_AFFX-r2-Bs-dap_5_signal12.898972
NoiseAvg:2.70,Std:0.12,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.826371
#P15218
Spike_AFFX-r2-Bs-phe_M_signal38.130821
Corner-Avg:17062,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal110.243607
Spike_AFFX-r2-Ec-bioB_3_signal116.363861
Spike_AFFX-r2-Bs-lys_M_signal23.148945
Spike_AFFX-r2-P1-cre_3_signal5536.187500
Spike_AFFX-r2-Bs-lys_3-5-ratio1.827379
Spike_AFFX-r2-Bs-dap_M_signal124.641174
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.692367
Spike_AFFX-r2-Ec-bioB_avg-signal97.254814
Spike_AFFX-r2-Bs-thr_avg-signal55.086025
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1139.983643
Spike_AFFX-r2-Bs-phe_5_signal21.864811
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1612.833862
RawQ2.483715
Spike_AFFX-r2-Bs-lys_5_signal23.505545
Signal(A)4.389607
%A31.674704
Signal(All)142.636932
Corner+Avg:161,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal318.563934
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal59.308079
Spike_AFFX-r2-Ec-bioD_avg-signal1376.408691
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.716354
Spike_AFFX-r2-Bs-lys_avg-signal29.869347
Spike_AFFX-r2-P1-cre_avg-signal4918.646484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal98.665154
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal39.767902
Spike_AFFX-r2-Bs-dap_3_signal252.243774
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.414787
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal278.145813
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.953548
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.145313
Spike_AFFX-r2-Bs-thr_M_signal53.766556
Signal(P)211.314758
Spike_AFFX-r2-Bs-phe_3-5-ratio2.712490
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14709,Count:9
Spike_AFFX-r2-P1-cre_5_signal4301.105469
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7225
Signal(M)16.472658
BackgroundAvg:87.67,Std:0.46,Min:86.0,Max:88.7
Spike_AFFX-r2-Ec-bioC_avg-signal298.354858
Spike_AFFX-r2-Bs-dap_avg-signal129.927979
Spike_AFFX-r2-Bs-dap_3-5-ratio19.555340
Spike_AFFX-r2-Ec-bioB_5_signal65.156960
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.659571
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-13_Water_24h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-13_Water_24h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-13_Water_24h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.025594
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-ratio1.572851
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.216193
Spike_AFFX-r2-Bs-dap_5_signal94.048439
NoiseAvg:2.46,Std:0.07,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal32.425079
#P14477
Spike_AFFX-r2-Bs-phe_M_signal42.827385
Corner-Avg:11002,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal98.283958
Spike_AFFX-r2-Ec-bioB_3_signal91.851456
Spike_AFFX-r2-Bs-lys_M_signal25.414259
Spike_AFFX-r2-P1-cre_3_signal6052.043457
Spike_AFFX-r2-Bs-lys_3-5-ratio1.768363
Spike_AFFX-r2-Bs-dap_M_signal206.911438
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.953013
Spike_AFFX-r2-Ec-bioB_avg-signal88.553047
Spike_AFFX-r2-Bs-thr_avg-signal114.398445
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal904.545166
Spike_AFFX-r2-Bs-phe_5_signal38.916653
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1691.777588
RawQ2.225455
Spike_AFFX-r2-Bs-lys_5_signal35.248852
Signal(A)6.388035
%A34.436649
Signal(All)140.347733
Corner+Avg:93,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal293.062866
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal130.912476
Spike_AFFX-r2-Ec-bioD_avg-signal1298.161377
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.467777
Spike_AFFX-r2-Bs-lys_avg-signal40.998627
Spike_AFFX-r2-P1-cre_avg-signal4949.930176
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.095572
Spike_AFFX-r2-Bs-thr_3_signal225.452011
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal70.885506
Spike_AFFX-r2-Bs-dap_3_signal391.961884
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.870307
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal253.936279
#M478
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal62.332764
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.154080
Spike_AFFX-r2-Bs-thr_M_signal85.318253
Signal(P)216.980484
Spike_AFFX-r2-Bs-phe_3-5-ratio3.363919
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11347,Count:9
Spike_AFFX-r2-P1-cre_5_signal3847.816650
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7855
Signal(M)20.767990
BackgroundAvg:52.44,Std:0.43,Min:51.6,Max:54.0
Spike_AFFX-r2-Ec-bioC_avg-signal273.499573
Spike_AFFX-r2-Bs-dap_avg-signal230.973923
Spike_AFFX-r2-Bs-dap_3-5-ratio4.167660
Spike_AFFX-r2-Ec-bioB_5_signal75.523735
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.025594
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-14_Water_24h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-14_Water_24h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-14_Water_24h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.478804
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-ratio1.404843
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.133864
Spike_AFFX-r2-Bs-dap_5_signal68.150803
NoiseAvg:2.82,Std:0.08,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.242920
#P15862
Spike_AFFX-r2-Bs-phe_M_signal40.146702
Corner-Avg:16494,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.383003
Spike_AFFX-r2-Ec-bioB_3_signal82.704559
Spike_AFFX-r2-Bs-lys_M_signal20.994232
Spike_AFFX-r2-P1-cre_3_signal4268.991211
Spike_AFFX-r2-Bs-lys_3-5-ratio2.068146
Spike_AFFX-r2-Bs-dap_M_signal179.480316
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.204550
Spike_AFFX-r2-Ec-bioB_avg-signal82.009346
Spike_AFFX-r2-Bs-thr_avg-signal70.327278
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal805.120789
Spike_AFFX-r2-Bs-phe_5_signal33.811176
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1233.907715
RawQ2.445356
Spike_AFFX-r2-Bs-lys_5_signal25.461250
Signal(A)3.527948
%A28.978518
Signal(All)136.521408
Corner+Avg:163,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal262.188660
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal99.927567
Spike_AFFX-r2-Ec-bioD_avg-signal1019.514282
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.539673
Spike_AFFX-r2-Bs-lys_avg-signal33.037685
Spike_AFFX-r2-P1-cre_avg-signal3653.879395
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal125.598206
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal57.961811
Spike_AFFX-r2-Bs-dap_3_signal331.280304
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.532575
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal222.600296
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal52.657578
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.177845
Spike_AFFX-r2-Bs-thr_M_signal65.140724
Signal(P)194.563766
Spike_AFFX-r2-Bs-phe_3-5-ratio2.955460
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13840,Count:9
Spike_AFFX-r2-P1-cre_5_signal3038.767578
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6610
Signal(M)13.500384
BackgroundAvg:61.87,Std:0.42,Min:60.7,Max:62.8
Spike_AFFX-r2-Ec-bioC_avg-signal242.394470
Spike_AFFX-r2-Bs-dap_avg-signal192.970474
Spike_AFFX-r2-Bs-dap_3-5-ratio4.860989
Spike_AFFX-r2-Ec-bioB_5_signal72.940475
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.478804
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-15_Calcium_0h_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Aubry_1-15_Calcium_0h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-15_Calcium_0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.695232
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-ratio1.302287
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.224327
Spike_AFFX-r2-Bs-dap_5_signal99.593575
NoiseAvg:2.73,Std:0.11,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.415127
#P15495
Spike_AFFX-r2-Bs-phe_M_signal49.049187
Corner-Avg:15427,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.803596
Spike_AFFX-r2-Ec-bioB_3_signal82.652794
Spike_AFFX-r2-Bs-lys_M_signal29.214073
Spike_AFFX-r2-P1-cre_3_signal4458.093750
Spike_AFFX-r2-Bs-lys_3-5-ratio2.483705
Spike_AFFX-r2-Bs-dap_M_signal271.616089
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.924731
Spike_AFFX-r2-Ec-bioB_avg-signal80.321709
Spike_AFFX-r2-Bs-thr_avg-signal114.555809
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal885.729675
Spike_AFFX-r2-Bs-phe_5_signal38.817963
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1353.235840
RawQ2.470693
Spike_AFFX-r2-Bs-lys_5_signal29.990673
Signal(A)4.327310
%A30.390181
Signal(All)138.445923
Corner+Avg:133,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal281.279633
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal116.863518
Spike_AFFX-r2-Ec-bioD_avg-signal1119.482788
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.930733
Spike_AFFX-r2-Bs-lys_avg-signal44.564243
Spike_AFFX-r2-P1-cre_avg-signal3940.687500
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.679088
Spike_AFFX-r2-Bs-thr_3_signal210.616577
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal68.243553
Spike_AFFX-r2-Bs-dap_3_signal480.934448
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.527820
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal236.259186
#M383
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal74.487984
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.190555
Spike_AFFX-r2-Bs-thr_M_signal102.635719
Signal(P)201.459335
Spike_AFFX-r2-Bs-phe_3-5-ratio3.010553
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12742,Count:9
Spike_AFFX-r2-P1-cre_5_signal3423.281006
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6932
Signal(M)16.558830
BackgroundAvg:60.64,Std:0.39,Min:59.6,Max:62.0
Spike_AFFX-r2-Ec-bioC_avg-signal258.769409
Spike_AFFX-r2-Bs-dap_avg-signal284.048035
Spike_AFFX-r2-Bs-dap_3-5-ratio4.828970
Spike_AFFX-r2-Ec-bioB_5_signal67.508743
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.695232
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-16_Calcium_0h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-16_Calcium_0h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-16_Calcium_0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.152072
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-ratio1.300070
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.313062
Spike_AFFX-r2-Bs-dap_5_signal142.469238
NoiseAvg:2.31,Std:0.06,Min:2.1,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal59.853455
#P14739
Spike_AFFX-r2-Bs-phe_M_signal66.907005
Corner-Avg:8902,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal170.180267
Spike_AFFX-r2-Ec-bioB_3_signal117.769577
Spike_AFFX-r2-Bs-lys_M_signal49.581825
Spike_AFFX-r2-P1-cre_3_signal7754.182617
Spike_AFFX-r2-Bs-lys_3-5-ratio1.639300
Spike_AFFX-r2-Bs-dap_M_signal446.726868
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.287147
Spike_AFFX-r2-Ec-bioB_avg-signal125.880211
Spike_AFFX-r2-Bs-thr_avg-signal223.347839
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1431.690796
Spike_AFFX-r2-Bs-phe_5_signal58.553539
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2243.740234
RawQ2.324764
Spike_AFFX-r2-Bs-lys_5_signal43.661816
Signal(A)6.516705
%A33.454624
Signal(All)142.817093
Corner+Avg:82,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal563.939453
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal151.111420
Spike_AFFX-r2-Ec-bioD_avg-signal1837.715576
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.616394
Spike_AFFX-r2-Bs-lys_avg-signal54.939480
Spike_AFFX-r2-P1-cre_avg-signal6859.308105
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.928979
Spike_AFFX-r2-Bs-thr_3_signal436.160889
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal92.190651
Spike_AFFX-r2-Bs-dap_3_signal667.407593
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.567196
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal495.396240
#M440
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal71.574791
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.138360
Spike_AFFX-r2-Bs-thr_M_signal174.029205
Signal(P)216.956818
Spike_AFFX-r2-Bs-phe_3-5-ratio2.580739
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6196,Count:9
Spike_AFFX-r2-P1-cre_5_signal5964.433594
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7631
Signal(M)23.187616
BackgroundAvg:56.15,Std:0.39,Min:55.1,Max:57.1
Spike_AFFX-r2-Ec-bioC_avg-signal529.667847
Spike_AFFX-r2-Bs-dap_avg-signal418.867920
Spike_AFFX-r2-Bs-dap_3-5-ratio4.684573
Spike_AFFX-r2-Ec-bioB_5_signal89.690781
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.152072
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-17_Calcium_4h_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 ("Aubry_1-17_Calcium_4h_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: Aubry_1-17_Calcium_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.615964
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-ratio1.419839
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.393177
Spike_AFFX-r2-Bs-dap_5_signal117.156006
NoiseAvg:2.85,Std:0.10,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.921335
#P15537
Spike_AFFX-r2-Bs-phe_M_signal54.137314
Corner-Avg:17575,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal103.778191
Spike_AFFX-r2-Ec-bioB_3_signal87.150398
Spike_AFFX-r2-Bs-lys_M_signal28.770443
Spike_AFFX-r2-P1-cre_3_signal4234.225586
Spike_AFFX-r2-Bs-lys_3-5-ratio1.826262
Spike_AFFX-r2-Bs-dap_M_signal301.664368
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.693826
Spike_AFFX-r2-Ec-bioB_avg-signal84.494583
Spike_AFFX-r2-Bs-thr_avg-signal127.724556
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal735.331299
Spike_AFFX-r2-Bs-phe_5_signal59.577118
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1339.600342
RawQ2.595720
Spike_AFFX-r2-Bs-lys_5_signal31.688990
Signal(A)3.942357
%A30.306883
Signal(All)136.150391
Corner+Avg:153,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal294.255219
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal116.797447
Spike_AFFX-r2-Ec-bioD_avg-signal1037.465820
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.114861
Spike_AFFX-r2-Bs-lys_avg-signal39.443947
Spike_AFFX-r2-P1-cre_avg-signal3608.206055
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal251.276917
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal76.837288
Spike_AFFX-r2-Bs-dap_3_signal445.293854
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.821764
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.031601
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.872410
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.231031
Spike_AFFX-r2-Bs-thr_M_signal105.975441
Signal(P)197.779831
Spike_AFFX-r2-Bs-phe_3-5-ratio1.960441
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14048,Count:9
Spike_AFFX-r2-P1-cre_5_signal2982.186279
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6913
Signal(M)15.088253
BackgroundAvg:64.40,Std:0.77,Min:62.3,Max:65.8
Spike_AFFX-r2-Ec-bioC_avg-signal266.643402
Spike_AFFX-r2-Bs-dap_avg-signal288.038086
Spike_AFFX-r2-Bs-dap_3-5-ratio3.800862
Spike_AFFX-r2-Ec-bioB_5_signal62.555164
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.615964
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-18_Calcium_4h_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 ("Aubry_1-18_Calcium_4h_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: Aubry_1-18_Calcium_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.69364
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-ratio1.443827
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.458817
Spike_AFFX-r2-Bs-dap_5_signal233.544205
NoiseAvg:2.73,Std:0.06,Min:2.6,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal77.026276
#P15068
Spike_AFFX-r2-Bs-phe_M_signal109.686981
Corner-Avg:15099,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.522575
Spike_AFFX-r2-Ec-bioB_3_signal102.137108
Spike_AFFX-r2-Bs-lys_M_signal65.563850
Spike_AFFX-r2-P1-cre_3_signal5328.669434
Spike_AFFX-r2-Bs-lys_3-5-ratio1.916185
Spike_AFFX-r2-Bs-dap_M_signal592.808411
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.303599
Spike_AFFX-r2-Ec-bioB_avg-signal97.224449
Spike_AFFX-r2-Bs-thr_avg-signal281.880585
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1006.364014
Spike_AFFX-r2-Bs-phe_5_signal125.771065
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1622.831055
RawQ2.580743
Spike_AFFX-r2-Bs-lys_5_signal65.458687
Signal(A)4.300267
%A32.235863
Signal(All)140.336655
Corner+Avg:132,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal286.439667
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal265.677063
Spike_AFFX-r2-Ec-bioD_avg-signal1314.597534
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.058746
Spike_AFFX-r2-Bs-lys_avg-signal85.484497
Spike_AFFX-r2-P1-cre_avg-signal4509.663086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal562.569031
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal167.045029
Spike_AFFX-r2-Bs-dap_3_signal969.941528
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.612569
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal284.891602
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal125.430946
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.005434
Spike_AFFX-r2-Bs-thr_M_signal206.046448
Signal(P)209.931305
Spike_AFFX-r2-Bs-phe_3-5-ratio2.112386
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12639,Count:9
Spike_AFFX-r2-P1-cre_5_signal3690.656738
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7353
Signal(M)15.974767
BackgroundAvg:65.25,Std:0.60,Min:64.3,Max:66.9
Spike_AFFX-r2-Ec-bioC_avg-signal285.665649
Spike_AFFX-r2-Bs-dap_avg-signal598.764709
Spike_AFFX-r2-Bs-dap_3-5-ratio4.153139
Spike_AFFX-r2-Ec-bioB_5_signal70.013649
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.693640
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-19_Calcium_8h_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 ("Aubry_1-19_Calcium_8h_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: Aubry_1-19_Calcium_8h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.692791
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-ratio1.348109
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.088940
Spike_AFFX-r2-Bs-dap_5_signal68.545013
NoiseAvg:3.31,Std:0.14,Min:3.0,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal27.659693
#P14621
Spike_AFFX-r2-Bs-phe_M_signal47.208214
Corner-Avg:15775,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal116.063705
Spike_AFFX-r2-Ec-bioB_3_signal84.853806
Spike_AFFX-r2-Bs-lys_M_signal23.167345
Spike_AFFX-r2-P1-cre_3_signal4768.635254
Spike_AFFX-r2-Bs-lys_3-5-ratio3.155896
Spike_AFFX-r2-Bs-dap_M_signal199.655533
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.607515
Spike_AFFX-r2-Ec-bioB_avg-signal92.946930
Spike_AFFX-r2-Bs-thr_avg-signal85.531044
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal917.109619
Spike_AFFX-r2-Bs-phe_5_signal15.642446
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1447.495728
RawQ2.830135
Spike_AFFX-r2-Bs-lys_5_signal15.738277
Signal(A)5.112849
%A34.199913
Signal(All)139.655640
Corner+Avg:139,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal298.573700
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal81.448639
Spike_AFFX-r2-Ec-bioD_avg-signal1182.302734
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.099083
Spike_AFFX-r2-Bs-lys_avg-signal29.524664
Spike_AFFX-r2-P1-cre_avg-signal4152.956543
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.701008
Spike_AFFX-r2-Bs-thr_3_signal155.102142
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.099766
Spike_AFFX-r2-Bs-dap_3_signal345.204010
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.578324
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal257.266449
#M388
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.668365
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.160562
Spike_AFFX-r2-Bs-thr_M_signal73.831314
Signal(P)214.652206
Spike_AFFX-r2-Bs-phe_3-5-ratio5.206899
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12279,Count:9
Spike_AFFX-r2-P1-cre_5_signal3537.278076
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7801
Signal(M)18.633457
BackgroundAvg:74.80,Std:0.85,Min:72.6,Max:76.6
Spike_AFFX-r2-Ec-bioC_avg-signal277.920074
Spike_AFFX-r2-Bs-dap_avg-signal204.468185
Spike_AFFX-r2-Bs-dap_3-5-ratio5.036165
Spike_AFFX-r2-Ec-bioB_5_signal77.923286
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.692791
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-20_Calcium_8h_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 ("Aubry_1-20_Calcium_8h_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: Aubry_1-20_Calcium_8h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.638433
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-ratio1.263258
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.963537
Spike_AFFX-r2-Bs-dap_5_signal98.500305
NoiseAvg:2.55,Std:0.09,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.878998
#P14378
Spike_AFFX-r2-Bs-phe_M_signal44.495106
Corner-Avg:9366,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.298248
Spike_AFFX-r2-Ec-bioB_3_signal66.665176
Spike_AFFX-r2-Bs-lys_M_signal19.110342
Spike_AFFX-r2-P1-cre_3_signal4489.731934
Spike_AFFX-r2-Bs-lys_3-5-ratio1.990899
Spike_AFFX-r2-Bs-dap_M_signal362.016327
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.416468
Spike_AFFX-r2-Ec-bioB_avg-signal77.383812
Spike_AFFX-r2-Bs-thr_avg-signal164.247223
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal676.168518
Spike_AFFX-r2-Bs-phe_5_signal43.170322
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1289.810791
RawQ2.378836
Spike_AFFX-r2-Bs-lys_5_signal29.080078
Signal(A)4.135948
%A35.221394
Signal(All)138.487427
Corner+Avg:94,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal326.015472
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal98.616142
Spike_AFFX-r2-Ec-bioD_avg-signal982.989624
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.033756
Spike_AFFX-r2-Bs-lys_avg-signal35.361973
Spike_AFFX-r2-P1-cre_avg-signal4021.910156
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.744849
Spike_AFFX-r2-Bs-thr_3_signal341.112610
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal62.093857
Spike_AFFX-r2-Bs-dap_3_signal543.466736
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.907529
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal271.187500
#M398
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.895500
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.202177
Spike_AFFX-r2-Bs-thr_M_signal121.750046
Signal(P)216.970215
Spike_AFFX-r2-Bs-phe_3-5-ratio2.284350
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7147,Count:9
Spike_AFFX-r2-P1-cre_5_signal3554.088623
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8034
Signal(M)15.256608
BackgroundAvg:62.07,Std:0.59,Min:60.8,Max:63.4
Spike_AFFX-r2-Ec-bioC_avg-signal298.601501
Spike_AFFX-r2-Bs-dap_avg-signal334.661102
Spike_AFFX-r2-Bs-dap_3-5-ratio5.517412
Spike_AFFX-r2-Ec-bioB_5_signal69.188004
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.638433
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-21_Calcium_12h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-21_Calcium_12h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-21_Calcium_12h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.626936
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-ratio1.328270
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.436610
Spike_AFFX-r2-Bs-dap_5_signal23.172989
NoiseAvg:2.62,Std:0.09,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.580202
#P14361
Spike_AFFX-r2-Bs-phe_M_signal17.517193
Corner-Avg:8591,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal73.855164
Spike_AFFX-r2-Ec-bioB_3_signal70.933937
Spike_AFFX-r2-Bs-lys_M_signal7.930358
Spike_AFFX-r2-P1-cre_3_signal4096.557617
Spike_AFFX-r2-Bs-lys_3-5-ratio2.869885
Spike_AFFX-r2-Bs-dap_M_signal119.545525
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.441012
Spike_AFFX-r2-Ec-bioB_avg-signal64.721664
Spike_AFFX-r2-Bs-thr_avg-signal58.846802
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal681.208679
Spike_AFFX-r2-Bs-phe_5_signal7.746637
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1110.118530
RawQ2.368522
Spike_AFFX-r2-Bs-lys_5_signal10.239338
Signal(A)4.652081
%A35.190704
Signal(All)137.348480
Corner+Avg:78,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal277.077057
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.524300
Spike_AFFX-r2-Ec-bioD_avg-signal895.663574
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.959229
Spike_AFFX-r2-Bs-lys_avg-signal15.851808
Spike_AFFX-r2-P1-cre_avg-signal3590.343750
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.850066
Spike_AFFX-r2-Bs-thr_3_signal123.906807
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.262709
Spike_AFFX-r2-Bs-dap_3_signal240.847458
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.629631
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal260.794861
#M422
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.385727
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.062433
Spike_AFFX-r2-Bs-thr_M_signal44.053391
Signal(P)215.095810
Spike_AFFX-r2-Bs-phe_3-5-ratio6.522095
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7095,Count:9
Spike_AFFX-r2-P1-cre_5_signal3084.129639
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8027
Signal(M)15.605861
BackgroundAvg:80.67,Std:0.99,Min:79.2,Max:84.0
Spike_AFFX-r2-Ec-bioC_avg-signal268.935974
Spike_AFFX-r2-Bs-dap_avg-signal127.855324
Spike_AFFX-r2-Bs-dap_3-5-ratio10.393456
Spike_AFFX-r2-Ec-bioB_5_signal49.375904
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.626936
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-22_Calcium_12h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-22_Calcium_12h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-22_Calcium_12h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.797081
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-ratio1.294276
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.196256
Spike_AFFX-r2-Bs-dap_5_signal174.769974
NoiseAvg:2.74,Std:0.23,Min:2.5,Max:4.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal72.941078
#P14760
Spike_AFFX-r2-Bs-phe_M_signal87.771858
Corner-Avg:9714,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal145.722549
Spike_AFFX-r2-Ec-bioB_3_signal112.083313
Spike_AFFX-r2-Bs-lys_M_signal40.799110
Spike_AFFX-r2-P1-cre_3_signal6169.300781
Spike_AFFX-r2-Bs-lys_3-5-ratio1.832958
Spike_AFFX-r2-Bs-dap_M_signal638.611450
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.788491
Spike_AFFX-r2-Ec-bioB_avg-signal117.166969
Spike_AFFX-r2-Bs-thr_avg-signal229.357803
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1191.059204
Spike_AFFX-r2-Bs-phe_5_signal72.012810
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1871.530884
RawQ2.473488
Spike_AFFX-r2-Bs-lys_5_signal60.870865
Signal(A)5.445065
%A33.559841
Signal(All)142.205002
Corner+Avg:100,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal425.023834
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal214.856400
Spike_AFFX-r2-Ec-bioD_avg-signal1531.295044
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.708458
Spike_AFFX-r2-Bs-lys_avg-signal71.081245
Spike_AFFX-r2-P1-cre_avg-signal5467.951660
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.731697
Spike_AFFX-r2-Bs-thr_3_signal422.218781
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal124.880363
Spike_AFFX-r2-Bs-dap_3_signal1030.203247
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.571316
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal377.703156
#M395
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal111.573769
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.125285
Spike_AFFX-r2-Bs-thr_M_signal192.913544
Signal(P)216.389771
Spike_AFFX-r2-Bs-phe_3-5-ratio2.983586
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7152,Count:9
Spike_AFFX-r2-P1-cre_5_signal4766.602539
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7655
Signal(M)20.509325
BackgroundAvg:83.82,Std:0.58,Min:82.5,Max:85.2
Spike_AFFX-r2-Ec-bioC_avg-signal401.363495
Spike_AFFX-r2-Bs-dap_avg-signal614.528259
Spike_AFFX-r2-Bs-dap_3-5-ratio5.894624
Spike_AFFX-r2-Ec-bioB_5_signal93.695084
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.797081
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-23_Calcium_16h_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 ("Aubry_1-23_Calcium_16h_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: Aubry_1-23_Calcium_16h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.751635
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-ratio1.224985
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.857113
Spike_AFFX-r2-Bs-dap_5_signal89.605865
NoiseAvg:2.56,Std:0.06,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.290915
#P13991
Spike_AFFX-r2-Bs-phe_M_signal32.495071
Corner-Avg:11964,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.902306
Spike_AFFX-r2-Ec-bioB_3_signal75.399254
Spike_AFFX-r2-Bs-lys_M_signal19.731520
Spike_AFFX-r2-P1-cre_3_signal3358.093262
Spike_AFFX-r2-Bs-lys_3-5-ratio2.190274
Spike_AFFX-r2-Bs-dap_M_signal230.326416
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.000657
Spike_AFFX-r2-Ec-bioB_avg-signal67.300606
Spike_AFFX-r2-Bs-thr_avg-signal114.797356
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal584.904236
Spike_AFFX-r2-Bs-phe_5_signal43.820095
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1119.826050
RawQ2.419588
Spike_AFFX-r2-Bs-lys_5_signal24.895359
Signal(A)4.553803
%A36.953091
Signal(All)136.023987
Corner+Avg:126,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal233.682419
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal115.854759
Spike_AFFX-r2-Ec-bioD_avg-signal852.365112
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.337132
Spike_AFFX-r2-Bs-lys_avg-signal33.051517
Spike_AFFX-r2-P1-cre_avg-signal3049.714111
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.709776
Spike_AFFX-r2-Bs-thr_3_signal242.084167
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal64.056641
Spike_AFFX-r2-Bs-dap_3_signal437.284546
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.914546
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal208.210846
#M390
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal54.527672
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.122335
Spike_AFFX-r2-Bs-thr_M_signal85.016968
Signal(P)218.565308
Spike_AFFX-r2-Bs-phe_3-5-ratio2.643873
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11083,Count:9
Spike_AFFX-r2-P1-cre_5_signal2741.334961
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8429
Signal(M)16.348751
BackgroundAvg:82.84,Std:0.54,Min:81.7,Max:84.2
Spike_AFFX-r2-Ec-bioC_avg-signal220.946625
Spike_AFFX-r2-Bs-dap_avg-signal252.405594
Spike_AFFX-r2-Bs-dap_3-5-ratio4.880088
Spike_AFFX-r2-Ec-bioB_5_signal40.600250
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.751635
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-24_Calcium_16h_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 ("Aubry_1-24_Calcium_16h_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: Aubry_1-24_Calcium_16h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.657642
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-ratio1.339674
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.121481
Spike_AFFX-r2-Bs-dap_5_signal97.118172
NoiseAvg:2.62,Std:0.06,Min:2.5,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.855597
#P14179
Spike_AFFX-r2-Bs-phe_M_signal31.869759
Corner-Avg:13489,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.894348
Spike_AFFX-r2-Ec-bioB_3_signal67.711449
Spike_AFFX-r2-Bs-lys_M_signal19.057442
Spike_AFFX-r2-P1-cre_3_signal4094.746582
Spike_AFFX-r2-Bs-lys_3-5-ratio2.163805
Spike_AFFX-r2-Bs-dap_M_signal214.089630
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.086084
Spike_AFFX-r2-Ec-bioB_avg-signal72.660881
Spike_AFFX-r2-Bs-thr_avg-signal94.809448
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal780.570496
Spike_AFFX-r2-Bs-phe_5_signal25.255054
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1145.078613
RawQ2.345575
Spike_AFFX-r2-Bs-lys_5_signal24.700218
Signal(A)4.135106
%A36.203419
Signal(All)137.599426
Corner+Avg:116,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal250.093185
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal82.212708
Spike_AFFX-r2-Ec-bioD_avg-signal962.824585
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.161331
Spike_AFFX-r2-Bs-lys_avg-signal32.401371
Spike_AFFX-r2-P1-cre_avg-signal3575.635742
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.635248
Spike_AFFX-r2-Bs-thr_3_signal200.265228
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal46.445843
Spike_AFFX-r2-Bs-dap_3_signal414.599548
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.466977
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal217.324371
#M373
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.446449
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.150783
Spike_AFFX-r2-Bs-thr_M_signal64.307518
Signal(P)218.573212
Spike_AFFX-r2-Bs-phe_3-5-ratio3.255297
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10686,Count:9
Spike_AFFX-r2-P1-cre_5_signal3056.525146
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8258
Signal(M)14.331665
BackgroundAvg:83.87,Std:0.53,Min:82.3,Max:85.2
Spike_AFFX-r2-Ec-bioC_avg-signal233.708771
Spike_AFFX-r2-Bs-dap_avg-signal241.935791
Spike_AFFX-r2-Bs-dap_3-5-ratio4.269022
Spike_AFFX-r2-Ec-bioB_5_signal60.376827
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.657642
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-25_Calcium_20h_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 ("Aubry_1-25_Calcium_20h_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: Aubry_1-25_Calcium_20h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.691687
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-ratio1.183878
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.441321
Spike_AFFX-r2-Bs-dap_5_signal102.395668
NoiseAvg:2.39,Std:0.10,Min:2.1,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.969690
#P14775
Spike_AFFX-r2-Bs-phe_M_signal45.191624
Corner-Avg:10014,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal116.617470
Spike_AFFX-r2-Ec-bioB_3_signal107.355911
Spike_AFFX-r2-Bs-lys_M_signal26.920765
Spike_AFFX-r2-P1-cre_3_signal4947.417480
Spike_AFFX-r2-Bs-lys_3-5-ratio2.827397
Spike_AFFX-r2-Bs-dap_M_signal315.655457
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.971494
Spike_AFFX-r2-Ec-bioB_avg-signal99.485924
Spike_AFFX-r2-Bs-thr_avg-signal142.495773
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal966.735718
Spike_AFFX-r2-Bs-phe_5_signal42.760441
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1524.279419
RawQ2.352003
Spike_AFFX-r2-Bs-lys_5_signal23.534262
Signal(A)3.707197
%A33.700130
Signal(All)135.627930
Corner+Avg:133,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal386.962585
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal100.603539
Spike_AFFX-r2-Ec-bioD_avg-signal1245.507568
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.774223
Spike_AFFX-r2-Bs-lys_avg-signal38.998577
Spike_AFFX-r2-P1-cre_avg-signal4563.204590
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.525647
Spike_AFFX-r2-Bs-thr_3_signal288.871094
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal62.851868
Spike_AFFX-r2-Bs-dap_3_signal569.609192
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.576728
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal304.609741
#M348
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal66.540703
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.270355
Spike_AFFX-r2-Bs-thr_M_signal109.646553
Signal(P)207.099960
Spike_AFFX-r2-Bs-phe_3-5-ratio2.352725
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8421,Count:9
Spike_AFFX-r2-P1-cre_5_signal4178.991699
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7687
Signal(M)15.155116
BackgroundAvg:81.58,Std:0.50,Min:80.3,Max:82.9
Spike_AFFX-r2-Ec-bioC_avg-signal345.786163
Spike_AFFX-r2-Bs-dap_avg-signal329.220123
Spike_AFFX-r2-Bs-dap_3-5-ratio5.562825
Spike_AFFX-r2-Ec-bioB_5_signal74.484367
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.691687
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-26_Calcium_20h_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 ("Aubry_1-26_Calcium_20h_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: Aubry_1-26_Calcium_20h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.072925
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-ratio1.256674
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.191143
Spike_AFFX-r2-Bs-dap_5_signal320.204071
NoiseAvg:2.49,Std:0.05,Min:2.3,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal71.054153
#P14219
Spike_AFFX-r2-Bs-phe_M_signal112.488441
Corner-Avg:15167,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal204.423325
Spike_AFFX-r2-Ec-bioB_3_signal174.579361
Spike_AFFX-r2-Bs-lys_M_signal69.010262
Spike_AFFX-r2-P1-cre_3_signal8507.301758
Spike_AFFX-r2-Bs-lys_3-5-ratio1.612862
Spike_AFFX-r2-Bs-dap_M_signal670.240967
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.844796
Spike_AFFX-r2-Ec-bioB_avg-signal175.189087
Spike_AFFX-r2-Bs-thr_avg-signal301.291687
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1767.540649
Spike_AFFX-r2-Bs-phe_5_signal117.184563
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2792.700928
RawQ2.351840
Spike_AFFX-r2-Bs-lys_5_signal88.001579
Signal(A)6.531568
%A35.769398
Signal(All)138.319794
Corner+Avg:123,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal604.315491
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal291.715454
Spike_AFFX-r2-Ec-bioD_avg-signal2280.120850
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.336693
Spike_AFFX-r2-Bs-lys_avg-signal99.648766
Spike_AFFX-r2-P1-cre_avg-signal7638.498047
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.893906
Spike_AFFX-r2-Bs-thr_3_signal557.405334
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal173.796143
Spike_AFFX-r2-Bs-dap_3_signal1256.646362
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.579993
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal512.853088
#M432
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal141.934433
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.178340
Spike_AFFX-r2-Bs-thr_M_signal275.415588
Signal(P)217.457428
Spike_AFFX-r2-Bs-phe_3-5-ratio2.489368
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14002,Count:9
Spike_AFFX-r2-P1-cre_5_signal6769.694824
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8159
Signal(M)22.584085
BackgroundAvg:83.15,Std:0.42,Min:81.9,Max:83.9
Spike_AFFX-r2-Ec-bioC_avg-signal558.584290
Spike_AFFX-r2-Bs-dap_avg-signal749.030457
Spike_AFFX-r2-Bs-dap_3-5-ratio3.924517
Spike_AFFX-r2-Ec-bioB_5_signal146.564575
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.072925
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-27_Calcium_24h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Aubry_1-27_Calcium_24h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-27_Calcium_24h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.593915
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-ratio1.354713
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.260606
Spike_AFFX-r2-Bs-dap_5_signal90.344536
NoiseAvg:3.03,Std:0.10,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.434277
#P14588
Spike_AFFX-r2-Bs-phe_M_signal44.092468
Corner-Avg:15523,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal87.039085
Spike_AFFX-r2-Ec-bioB_3_signal77.995461
Spike_AFFX-r2-Bs-lys_M_signal30.552155
Spike_AFFX-r2-P1-cre_3_signal4408.389648
Spike_AFFX-r2-Bs-lys_3-5-ratio2.540384
Spike_AFFX-r2-Bs-dap_M_signal214.997986
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.798308
Spike_AFFX-r2-Ec-bioB_avg-signal75.635323
Spike_AFFX-r2-Bs-thr_avg-signal101.283318
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal831.986084
Spike_AFFX-r2-Bs-phe_5_signal28.332996
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1170.213745
RawQ2.654890
Spike_AFFX-r2-Bs-lys_5_signal26.022038
Signal(A)4.303936
%A34.533100
Signal(All)136.568939
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal241.045410
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal77.637672
Spike_AFFX-r2-Ec-bioD_avg-signal1001.099915
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.954407
Spike_AFFX-r2-Bs-lys_avg-signal40.893387
Spike_AFFX-r2-P1-cre_avg-signal3831.251465
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal193.304977
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal50.021046
Spike_AFFX-r2-Bs-dap_3_signal456.545166
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.406530
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal207.013290
#M345
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal66.105965
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.164396
Spike_AFFX-r2-Bs-thr_M_signal82.110703
Signal(P)210.826080
Spike_AFFX-r2-Bs-phe_3-5-ratio2.740186
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12841,Count:9
Spike_AFFX-r2-P1-cre_5_signal3254.113281
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7877
Signal(M)16.534781
BackgroundAvg:93.33,Std:0.86,Min:91.4,Max:95.2
Spike_AFFX-r2-Ec-bioC_avg-signal224.029358
Spike_AFFX-r2-Bs-dap_avg-signal253.962570
Spike_AFFX-r2-Bs-dap_3-5-ratio5.053379
Spike_AFFX-r2-Ec-bioB_5_signal61.871426
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.593915
NF1.000000
HZ4
Tau0.015000

Slide: Aubry_1-28_Calcium_24h_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("Aubry_1-28_Calcium_24h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Aubry_1-28_Calcium_24h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 d
Growth Conditions:
Stratification2 days 4dC. dark
Sterilisation50% NaHyCl
ProtocolSeeds grown in LL 120 umol 20d for 15d Harvesting started on the subjective dawn
Percentage Agrose.8
Substrate Sterilising Procedureautoclave
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent manufactured by Sanyo. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: From the subjective dawn, a calcium ramp was applied, every hour from 0.5, 1, 5, 10, 20, 50, 60 mM then in water the following hours.
Additional Organism Information:
Sample Descriptionbulk of 4-6 seedlings, at 2 leaf stage
Other Information:
Timecourse start proceduresubjective dawn

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.01329
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-ratio1.341537
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.274335
Spike_AFFX-r2-Bs-dap_5_signal170.047852
NoiseAvg:2.61,Std:0.05,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal54.142414
#P13948
Spike_AFFX-r2-Bs-phe_M_signal92.940735
Corner-Avg:15335,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal189.908249
Spike_AFFX-r2-Ec-bioB_3_signal143.294708
Spike_AFFX-r2-Bs-lys_M_signal63.850525
Spike_AFFX-r2-P1-cre_3_signal7679.045898
Spike_AFFX-r2-Bs-lys_3-5-ratio1.998110
Spike_AFFX-r2-Bs-dap_M_signal552.888733
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.430282
Spike_AFFX-r2-Ec-bioB_avg-signal148.549881
Spike_AFFX-r2-Bs-thr_avg-signal292.035156
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1625.207642
Spike_AFFX-r2-Bs-phe_5_signal109.797981
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2407.464600
RawQ2.590226
Spike_AFFX-r2-Bs-lys_5_signal57.978935
Signal(A)6.022145
%A37.093380
Signal(All)141.481735
Corner+Avg:152,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal486.256287
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal237.265366
Spike_AFFX-r2-Ec-bioD_avg-signal2016.336182
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.148621
Spike_AFFX-r2-Bs-lys_avg-signal79.225922
Spike_AFFX-r2-P1-cre_avg-signal6701.554688
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.758001
Spike_AFFX-r2-Bs-thr_3_signal618.863037
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal146.668030
Spike_AFFX-r2-Bs-dap_3_signal1025.309814
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.481327
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal394.852356
#M401
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal115.848305
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.231489
Spike_AFFX-r2-Bs-thr_M_signal203.100052
Signal(P)227.052887
Spike_AFFX-r2-Bs-phe_3-5-ratio2.160927
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13240,Count:9
Spike_AFFX-r2-P1-cre_5_signal5724.063965
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8461
Signal(M)23.220528
BackgroundAvg:88.34,Std:0.43,Min:87.2,Max:89.3
Spike_AFFX-r2-Ec-bioC_avg-signal440.554321
Spike_AFFX-r2-Bs-dap_avg-signal582.748779
Spike_AFFX-r2-Bs-dap_3-5-ratio6.029537
Spike_AFFX-r2-Ec-bioB_5_signal112.446678
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.013290
NF1.000000
HZ4
Tau0.015000


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