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Experiment: Heat stress-30h

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-619

We applied 30 hours long heat stress to Arabidopsis Col plants with an aim to study the effects of heat stress on chromatin, epigenome stability and maintenance of transcriptional gene silencing.

About the Experimenter

Name: Ales Pecinka
Head of Lab Name: Ortrun Mittelsten Scheid
Lab:
Address:Gregor Mendel Institute (GMI)
Dr. Borh-Gasse 3, Vienna
Postcode: A-1030
Country: Austria
 

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

About this Experiment

Experiment Type: time_series_design;growth_condition_design
Number of Slides:8
 
Experimental Parameters:
parametertimepoint
parameterTemperature
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Pecinka: Heat stress-30h

Slide: Pecinka_619-1_22°C-no-recovery_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 ("Pecinka_619-1_22°C-no-recovery_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: Pecinka_619-1_22°C-no-recovery_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 0 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
ProtocolCold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 days in Percival growth chambers at 16h light / 8h dark cycles and 22°C.
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.04
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment22°C 0 days recovery
Additional Organism Information:
Time'0 days of recovery' is the first sample in this timecouse and is defined as a timetpoint immediately after the end of heat stress treatment
Sample descriptionSample was derived from a pool of 50 17-day old seedlings with no apparent phenotype
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.865038
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-ratio1.359354
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.462661
Spike_AFFX-r2-Bs-dap_5_signal28.127422
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_signal12.361908
#P14541
Spike_AFFX-r2-Bs-phe_M_signal35.984295
Corner-Avg:14177,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal104.846443
Spike_AFFX-r2-Ec-bioB_3_signal83.866402
Spike_AFFX-r2-Bs-lys_M_signal16.652771
Spike_AFFX-r2-P1-cre_3_signal5368.563965
Spike_AFFX-r2-Bs-lys_3-5-ratio2.486789
Spike_AFFX-r2-Bs-dap_M_signal138.210495
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.598066
Spike_AFFX-r2-Ec-bioB_avg-signal82.017036
Spike_AFFX-r2-Bs-thr_avg-signal40.783695
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1228.947144
Spike_AFFX-r2-Bs-phe_5_signal21.641924
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1954.804565
RawQ2.241093
Spike_AFFX-r2-Bs-lys_5_signal19.330503
Signal(A)4.605634
%A34.568172
Signal(All)146.859100
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal272.627197
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal74.777298
Spike_AFFX-r2-Ec-bioD_avg-signal1591.875854
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.748356
Spike_AFFX-r2-Bs-lys_avg-signal28.018057
Spike_AFFX-r2-P1-cre_avg-signal4658.956055
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.683472
Spike_AFFX-r2-Bs-thr_3_signal81.564690
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-signal44.134506
Spike_AFFX-r2-Bs-dap_3_signal303.587677
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.590634
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal287.698669
#M384
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.070892
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.947614
Spike_AFFX-r2-Bs-thr_M_signal28.424492
Signal(P)227.415512
Spike_AFFX-r2-Bs-phe_3-5-ratio3.455206
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11697,Count:9
Spike_AFFX-r2-P1-cre_5_signal3949.348389
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7885
Signal(M)17.426195
BackgroundAvg:50.98,Std:0.48,Min:50.3,Max:52.9
Spike_AFFX-r2-Ec-bioC_avg-signal280.162933
Spike_AFFX-r2-Bs-dap_avg-signal156.641861
Spike_AFFX-r2-Bs-dap_3-5-ratio10.793299
Spike_AFFX-r2-Ec-bioB_5_signal57.338253
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.865038
NF1.000000
HZ4
Tau0.015000

Slide: Pecinka_619-2_22°C-no-recovery_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 ("Pecinka_619-2_22°C-no-recovery_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: Pecinka_619-2_22°C-no-recovery_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 0 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
ProtocolCold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 days in Percival growth chambers at 16h light / 8h dark cycles and 22°C.
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.04
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment22°C 0 days recovery
Additional Organism Information:
Time'0 days of recovery' is the first sample in this timecouse and is defined as a timetpoint immediately after the end of heat stress treatment
Sample descriptionSample was derived from a pool of 50 17-day old seedlings with no apparent phenotype
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.98103
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-ratio1.299354
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.099159
Spike_AFFX-r2-Bs-dap_5_signal29.448700
NoiseAvg:2.27,Std:0.04,Min:2.1,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.732162
#P14308
Spike_AFFX-r2-Bs-phe_M_signal24.678854
Corner-Avg:12569,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal101.577362
Spike_AFFX-r2-Ec-bioB_3_signal71.993767
Spike_AFFX-r2-Bs-lys_M_signal13.987856
Spike_AFFX-r2-P1-cre_3_signal5242.923828
Spike_AFFX-r2-Bs-lys_3-5-ratio1.976513
Spike_AFFX-r2-Bs-dap_M_signal96.483749
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.709033
Spike_AFFX-r2-Ec-bioB_avg-signal79.690025
Spike_AFFX-r2-Bs-thr_avg-signal24.984865
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1225.284424
Spike_AFFX-r2-Bs-phe_5_signal19.045900
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1813.202148
RawQ2.160103
Spike_AFFX-r2-Bs-lys_5_signal16.749765
Signal(A)5.003937
%A35.458134
Signal(All)146.507156
Corner+Avg:107,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal265.638641
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal49.145027
Spike_AFFX-r2-Ec-bioD_avg-signal1519.243286
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.726875
Spike_AFFX-r2-Bs-lys_avg-signal21.281250
Spike_AFFX-r2-P1-cre_avg-signal4638.973633
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.814993
Spike_AFFX-r2-Bs-thr_3_signal51.898460
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-signal30.956594
Spike_AFFX-r2-Bs-dap_3_signal180.812973
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.479821
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal259.377228
#M414
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.106129
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.024140
Spike_AFFX-r2-Bs-thr_M_signal16.323975
Signal(P)230.180603
Spike_AFFX-r2-Bs-phe_3-5-ratio2.580347
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10983,Count:9
Spike_AFFX-r2-P1-cre_5_signal4035.023682
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8088
Signal(M)19.160618
BackgroundAvg:51.34,Std:0.34,Min:50.3,Max:52.2
Spike_AFFX-r2-Ec-bioC_avg-signal262.507935
Spike_AFFX-r2-Bs-dap_avg-signal102.248474
Spike_AFFX-r2-Bs-dap_3-5-ratio6.139931
Spike_AFFX-r2-Ec-bioB_5_signal65.498932
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.981030
NF1.000000
HZ4
Tau0.015000

Slide: Pecinka_619-3_37°C-no-recovery_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 ("Pecinka_619-3_37°C-no-recovery_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: Pecinka_619-3_37°C-no-recovery_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 0 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
ProtocolCold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 days in Percival growth chambers at 16h light / 8h dark cycles and 22°C.
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.04
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment37°C 0 days recovery
Additional Organism Information:
Time'0 days of recovery' is the first sample in this timecouse and is defined as a timetpoint immediately after the end of heat stress treatment
Sample descriptionSample was derived from a pool of 50 17-day old seedlings with no apparent phenotype
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.681492
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-ratio1.184692
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.035338
Spike_AFFX-r2-Bs-dap_5_signal39.536858
NoiseAvg:2.42,Std:0.07,Min:2.2,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_signal10.866113
#P15019
Spike_AFFX-r2-Bs-phe_M_signal22.884901
Corner-Avg:15259,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.988823
Spike_AFFX-r2-Ec-bioB_3_signal72.805214
Spike_AFFX-r2-Bs-lys_M_signal22.478872
Spike_AFFX-r2-P1-cre_3_signal3930.927002
Spike_AFFX-r2-Bs-lys_3-5-ratio1.656143
Spike_AFFX-r2-Bs-dap_M_signal113.959846
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.186036
Spike_AFFX-r2-Ec-bioB_avg-signal79.038086
Spike_AFFX-r2-Bs-thr_avg-signal25.050276
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal857.065918
Spike_AFFX-r2-Bs-phe_5_signal27.019222
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1521.595581
RawQ2.256431
Spike_AFFX-r2-Bs-lys_5_signal21.162682
Signal(A)3.645424
%A32.740025
Signal(All)136.897217
Corner+Avg:119,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal229.024246
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal81.776337
Spike_AFFX-r2-Ec-bioD_avg-signal1189.330811
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.843925
Spike_AFFX-r2-Bs-lys_avg-signal26.229994
Spike_AFFX-r2-P1-cre_avg-signal3624.514160
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.416046
Spike_AFFX-r2-Bs-thr_3_signal45.485935
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-signal43.893490
Spike_AFFX-r2-Bs-dap_3_signal268.204437
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.775354
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal204.005936
#M323
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.048424
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.122635
Spike_AFFX-r2-Bs-thr_M_signal18.798782
Signal(P)205.796921
Spike_AFFX-r2-Bs-phe_3-5-ratio3.026598
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14987,Count:9
Spike_AFFX-r2-P1-cre_5_signal3318.101563
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7468
Signal(M)14.047661
BackgroundAvg:55.21,Std:0.77,Min:52.3,Max:57.1
Spike_AFFX-r2-Ec-bioC_avg-signal216.515091
Spike_AFFX-r2-Bs-dap_avg-signal140.567047
Spike_AFFX-r2-Bs-dap_3-5-ratio6.783656
Spike_AFFX-r2-Ec-bioB_5_signal70.320221
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.681492
NF1.000000
HZ4
Tau0.015000

Slide: Pecinka_619-4_37°C-no-recovery_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 ("Pecinka_619-4_37°C-no-recovery_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: Pecinka_619-4_37°C-no-recovery_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 0 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
Protocol
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.04
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment37°C 0 days recovery
Additional Organism Information:
Time'0 days of recovery' is the first sample in this timecouse and is defined as a timetpoint immediately after the end of heat stress treatment
Sample descriptionSample was derived from a pool of 50 17-day old seedlings with no apparent phenotype
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.665812
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-ratio1.183025
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.329296
Spike_AFFX-r2-Bs-dap_5_signal30.773632
NoiseAvg:2.52,Std:0.20,Min:2.2,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.916530
#P14947
Spike_AFFX-r2-Bs-phe_M_signal16.186895
Corner-Avg:12420,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.745087
Spike_AFFX-r2-Ec-bioB_3_signal72.044563
Spike_AFFX-r2-Bs-lys_M_signal16.897949
Spike_AFFX-r2-P1-cre_3_signal3926.851563
Spike_AFFX-r2-Bs-lys_3-5-ratio1.655172
Spike_AFFX-r2-Bs-dap_M_signal92.977180
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.918770
Spike_AFFX-r2-Ec-bioB_avg-signal70.329056
Spike_AFFX-r2-Bs-thr_avg-signal22.725107
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal926.391418
Spike_AFFX-r2-Bs-phe_5_signal22.926725
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1471.160767
RawQ2.341195
Spike_AFFX-r2-Bs-lys_5_signal13.451522
Signal(A)3.527982
%A32.976765
Signal(All)136.557770
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal238.176651
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal72.944229
Spike_AFFX-r2-Ec-bioD_avg-signal1198.776123
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.528275
Spike_AFFX-r2-Bs-lys_avg-signal17.538019
Spike_AFFX-r2-P1-cre_avg-signal3623.091553
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.494958
Spike_AFFX-r2-Bs-thr_3_signal50.596756
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-signal37.352619
Spike_AFFX-r2-Bs-dap_3_signal226.557449
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.588055
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal210.724640
#M341
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.264584
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.130274
Spike_AFFX-r2-Bs-thr_M_signal13.662038
Signal(P)206.312485
Spike_AFFX-r2-Bs-phe_3-5-ratio3.181624
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10858,Count:9
Spike_AFFX-r2-P1-cre_5_signal3319.331543
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7522
Signal(M)13.468202
BackgroundAvg:56.81,Std:0.85,Min:54.3,Max:58.5
Spike_AFFX-r2-Ec-bioC_avg-signal224.450653
Spike_AFFX-r2-Bs-dap_avg-signal116.769417
Spike_AFFX-r2-Bs-dap_3-5-ratio7.362064
Spike_AFFX-r2-Ec-bioB_5_signal54.197521
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.665812
NF1.000000
HZ4
Tau0.015000

Slide: Pecinka_619-5_22°C-2day-recovery_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 ("Pecinka_619-5_22°C-2day-recovery_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: Pecinka_619-5_22°C-2day-recovery_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 2 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
ProtocolCold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 + 2 (recovery) days in Percival growth chambers at 16h light / 8h dark cycles and 22°C.
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.06
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment22°C 2 days recovery
Additional Organism Information:
Time'0 days of recovery' is defined as a timetpoint immediately after the end of heat stress treatment. This is the second sample in my timecouse and was harvested 48 hours after the end of heat stress
Sample descriptionSample was derived from a pool of 50 17-day old seedlings with no apparent phenotype
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.697172
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-ratio1.302210
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.581265
Spike_AFFX-r2-Bs-dap_5_signal41.363373
NoiseAvg:2.38,Std:0.06,Min:2.2,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_signal4.947162
#P15149
Spike_AFFX-r2-Bs-phe_M_signal34.440109
Corner-Avg:17665,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal115.151993
Spike_AFFX-r2-Ec-bioB_3_signal118.492783
Spike_AFFX-r2-Bs-lys_M_signal19.757385
Spike_AFFX-r2-P1-cre_3_signal5557.469727
Spike_AFFX-r2-Bs-lys_3-5-ratio2.025009
Spike_AFFX-r2-Bs-dap_M_signal130.442444
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.298924
Spike_AFFX-r2-Ec-bioB_avg-signal102.860069
Spike_AFFX-r2-Bs-thr_avg-signal24.543306
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1411.409912
Spike_AFFX-r2-Bs-phe_5_signal22.002672
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2176.706055
RawQ2.186414
Spike_AFFX-r2-Bs-lys_5_signal22.108849
Signal(A)3.664713
%A32.213940
Signal(All)145.322739
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal296.707306
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal76.362755
Spike_AFFX-r2-Ec-bioD_avg-signal1794.057983
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.413857
Spike_AFFX-r2-Bs-lys_avg-signal28.878950
Spike_AFFX-r2-P1-cre_avg-signal4912.595215
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.372205
Spike_AFFX-r2-Bs-thr_3_signal46.003288
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-signal44.268513
Spike_AFFX-r2-Bs-dap_3_signal337.687042
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.542221
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal289.662994
#M313
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.770611
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.024319
Spike_AFFX-r2-Bs-thr_M_signal22.679472
Signal(P)216.737640
Spike_AFFX-r2-Bs-phe_3-5-ratio3.470613
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15921,Count:9
Spike_AFFX-r2-P1-cre_5_signal4267.720703
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7348
Signal(M)14.455878
BackgroundAvg:53.85,Std:1.21,Min:50.8,Max:56.1
Spike_AFFX-r2-Ec-bioC_avg-signal293.185150
Spike_AFFX-r2-Bs-dap_avg-signal169.830948
Spike_AFFX-r2-Bs-dap_3-5-ratio8.163915
Spike_AFFX-r2-Ec-bioB_5_signal74.935425
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.697172
NF1.000000
HZ4
Tau0.015000

Slide: Pecinka_619-6_22°C-2day-recovery_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 ("Pecinka_619-6_22°C-2day-recovery_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: Pecinka_619-6_22°C-2day-recovery_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 2 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
ProtocolCold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 + 2 (recovery) days in Percival growth chambers at 16h light / 8h dark cycles and 22°C.
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.06
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment22°C 2 days recovery
Additional Organism Information:
Time'0 days of recovery' is defined as a timetpoint immediately after the end of heat stress treatment. This is the second sample in my timecouse and was harvested 48 hours after the end of heat stress
Sample descriptionSample was derived from a pool of 50 17-day old seedlings with no apparent phenotype
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.808978
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-ratio1.186378
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.002570
Spike_AFFX-r2-Bs-dap_5_signal28.692944
NoiseAvg:2.44,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_signal9.474439
#P14707
Spike_AFFX-r2-Bs-phe_M_signal24.900017
Corner-Avg:12952,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.608231
Spike_AFFX-r2-Ec-bioB_3_signal72.657303
Spike_AFFX-r2-Bs-lys_M_signal11.600752
Spike_AFFX-r2-P1-cre_3_signal4642.800293
Spike_AFFX-r2-Bs-lys_3-5-ratio4.200938
Spike_AFFX-r2-Bs-dap_M_signal117.364380
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.190336
Spike_AFFX-r2-Ec-bioB_avg-signal76.578865
Spike_AFFX-r2-Bs-thr_avg-signal30.308905
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1065.607788
Spike_AFFX-r2-Bs-phe_5_signal19.029823
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1662.853882
RawQ2.327139
Spike_AFFX-r2-Bs-lys_5_signal12.067880
Signal(A)4.386629
%A33.910564
Signal(All)145.342911
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal274.067017
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal55.155720
Spike_AFFX-r2-Ec-bioD_avg-signal1364.230835
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.476105
Spike_AFFX-r2-Bs-lys_avg-signal24.788347
Spike_AFFX-r2-P1-cre_avg-signal4278.111816
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.613328
Spike_AFFX-r2-Bs-thr_3_signal58.649960
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-signal33.028522
Spike_AFFX-r2-Bs-dap_3_signal253.122040
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.560475
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.033356
#M368
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.696411
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.118489
Spike_AFFX-r2-Bs-thr_M_signal22.802315
Signal(P)222.712158
Spike_AFFX-r2-Bs-phe_3-5-ratio2.898383
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9581,Count:9
Spike_AFFX-r2-P1-cre_5_signal3913.423340
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7735
Signal(M)16.069374
BackgroundAvg:56.43,Std:1.27,Min:53.6,Max:59.2
Spike_AFFX-r2-Ec-bioC_avg-signal259.550171
Spike_AFFX-r2-Bs-dap_avg-signal133.059784
Spike_AFFX-r2-Bs-dap_3-5-ratio8.821753
Spike_AFFX-r2-Ec-bioB_5_signal72.471062
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.808978
NF1.000000
HZ4
Tau0.015000

Slide: Pecinka_619-7_37°C-2day-recovery_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 ("Pecinka_619-7_37°C-2day-recovery_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: Pecinka_619-7_37°C-2day-recovery_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 2 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
ProtocolCold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 days in Percival growth chambers at 16h light / 8h dark cycles and 22°C. Plants were stressed by heat (37°C) for 30 hours and subsequently returned to 22°C for 48h hours (2 days) of recovery.
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.06
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment37°C 2 days recovery
Additional Organism Information:
Time'0 days of recovery' is defined as a timetpoint immediately after the end of heat stress treatment. This is the second sample in my timecouse and was harvested 48 hours after the end of heat stress
Sample descriptionSample was derived from a pool of 50 20-day old seedlings with heat stress damage phenotype (partial loss of turgor, dying of the oldest leaves)
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.964673
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-ratio1.247110
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.456612
Spike_AFFX-r2-Bs-dap_5_signal27.828516
NoiseAvg:2.20,Std:0.05,Min:2.0,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal0.620532
#P14286
Spike_AFFX-r2-Bs-phe_M_signal22.504980
Corner-Avg:15594,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal122.993019
Spike_AFFX-r2-Ec-bioB_3_signal96.751915
Spike_AFFX-r2-Bs-lys_M_signal13.661205
Spike_AFFX-r2-P1-cre_3_signal5649.111328
Spike_AFFX-r2-Bs-lys_3-5-ratio3.097798
Spike_AFFX-r2-Bs-dap_M_signal88.812195
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio44.828281
Spike_AFFX-r2-Ec-bioB_avg-signal95.389160
Spike_AFFX-r2-Bs-thr_avg-signal20.305443
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1289.213623
Spike_AFFX-r2-Bs-phe_5_signal15.291082
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2099.575928
RawQ2.126202
Spike_AFFX-r2-Bs-lys_5_signal13.722334
Signal(A)5.078171
%A35.545815
Signal(All)148.729431
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal257.139252
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal45.610832
Spike_AFFX-r2-Ec-bioD_avg-signal1694.394775
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.630424
Spike_AFFX-r2-Bs-lys_avg-signal23.297522
Spike_AFFX-r2-P1-cre_avg-signal5089.435547
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.823761
Spike_AFFX-r2-Bs-thr_3_signal44.828281
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-signal27.802299
Spike_AFFX-r2-Bs-dap_3_signal223.039551
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.628571
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal260.294037
#M416
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.509022
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.987880
Spike_AFFX-r2-Bs-thr_M_signal15.467515
Signal(P)234.048981
Spike_AFFX-r2-Bs-phe_3-5-ratio2.982839
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11560,Count:9
Spike_AFFX-r2-P1-cre_5_signal4529.760254
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8108
Signal(M)18.559429
BackgroundAvg:52.00,Std:0.86,Min:50.5,Max:54.4
Spike_AFFX-r2-Ec-bioC_avg-signal258.716644
Spike_AFFX-r2-Bs-dap_avg-signal113.226753
Spike_AFFX-r2-Bs-dap_3-5-ratio8.014784
Spike_AFFX-r2-Ec-bioB_5_signal66.422562
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.964673
NF1.000000
HZ4
Tau0.015000

Slide: Pecinka_619-8_37°C-2day-recovery_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 ("Pecinka_619-8_37°C-2day-recovery_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: Pecinka_619-8_37°C-2day-recovery_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia (Col)
Stock Code:
Age: 2 days of recovery
Growth Conditions:
StratificationSeeds were dried after harvesting and cold-treated for minimum 7 days at 4°C
Sterilisation6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.
ProtocolCold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 days in Percival growth chambers at 16h light / 8h dark cycles and 22°C. Plants were stressed by heat (37°C) for 30 hours and subsequently returned to 22°C for 48h hours (2 days) of recovery.
LocationGrowth chamber
Growth substrate typeAgar
Growth mediumGamborg's B-5 basal salt mixture
Developmental Stage:
Developmental-stage1.06
Tissue: shoot (aerial parts)
in vivo Treatment:
Treatment37°C 2 days recovery
Additional Organism Information:
Time'0 days of recovery' is defined as a timetpoint immediately after the end of heat stress treatment. This is the second sample in my timecouse and was harvested 48 hours after the end of heat stress
Sample descriptionSample was derived from a pool of 50 20-day old seedlings with heat stress damage phenotype (partial loss of turgor, dying of the oldest leaves)
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.965178
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-ratio1.263276
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.425308
Spike_AFFX-r2-Bs-dap_5_signal31.245441
NoiseAvg:2.03,Std:0.08,Min:1.8,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.368659
#P14191
Spike_AFFX-r2-Bs-phe_M_signal26.205051
Corner-Avg:13690,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal118.943069
Spike_AFFX-r2-Ec-bioB_3_signal112.027557
Spike_AFFX-r2-Bs-lys_M_signal16.993254
Spike_AFFX-r2-P1-cre_3_signal5794.045410
Spike_AFFX-r2-Bs-lys_3-5-ratio2.776910
Spike_AFFX-r2-Bs-dap_M_signal113.190048
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.118349
Spike_AFFX-r2-Ec-bioB_avg-signal103.189827
Spike_AFFX-r2-Bs-thr_avg-signal20.219139
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1279.743286
Spike_AFFX-r2-Bs-phe_5_signal11.720762
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2302.875244
RawQ1.945047
Spike_AFFX-r2-Bs-lys_5_signal15.210248
Signal(A)4.708489
%A36.001755
Signal(All)148.262192
Corner+Avg:101,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal315.255005
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal48.485783
Spike_AFFX-r2-Ec-bioD_avg-signal1791.309326
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.213940
Spike_AFFX-r2-Bs-lys_avg-signal24.813665
Spike_AFFX-r2-P1-cre_avg-signal5190.285156
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.784305
Spike_AFFX-r2-Bs-thr_3_signal30.346708
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-signal28.803865
Spike_AFFX-r2-Bs-dap_3_signal264.509552
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.799482
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal276.290344
#M407
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.237492
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.141028
Spike_AFFX-r2-Bs-thr_M_signal22.942049
Signal(P)235.063705
Spike_AFFX-r2-Bs-phe_3-5-ratio4.136743
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12799,Count:9
Spike_AFFX-r2-P1-cre_5_signal4586.524414
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8212
Signal(M)18.195623
BackgroundAvg:71.41,Std:0.97,Min:69.4,Max:73.5
Spike_AFFX-r2-Ec-bioC_avg-signal295.772675
Spike_AFFX-r2-Bs-dap_avg-signal136.315018
Spike_AFFX-r2-Bs-dap_3-5-ratio8.465541
Spike_AFFX-r2-Ec-bioB_5_signal78.598854
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.965178
NF1.000000
HZ4
Tau0.015000


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