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Experiment: Expression changes during polyploidisation (2)

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-616

Polyploidisation is frequent in higher plants and contributed significantly to their evolution and adaptation. The sucess of polyploid plants seems to be due to diversification that is least in part generated by major changes in genome organisation and epigenetic regulation. The aim of this experiment is to analyse changes in global gene-expression occurring after autopolyploidisation of an Arabidopsis thaliana line carrying a HPT transgene. Mittelsten Scheid O. et al., PNAS, 1996 Mittelsten Scheid O. et al., Nature Genetics, 2003

About the Experimenter

Name: Tuncay Baubec
Head of Lab Name: Ortrun Mittelsten Scheid
Lab:
Address:Gregor Mendel Institute of Molecular Plant Biology
Austrian Academy of Sciences
Vienna - Austria
Postcode: 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: genetic_modification_design
Number of Slides:6
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Baubec: Expression changes during polyploidisation (2)

Slide: Baubec_616-1_tetraploid-lineC-S2_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 ("Baubec_616-1_tetraploid-lineC-S2_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: Baubec_616-1_tetraploid-lineC-S2_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C4S2
Stock Code:
Age: 17
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 21°C.
Percentage Agrose8
Plant Spacing50/plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumOwn medium: MS macro 50ml B5 micro 1ml ammonium iron citrate 50mg sucrose 10g MES 350mg 8% Agar 450ml
Lighting(Source: Fluorescent manufactured by Phillips. Intensity: 105µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: knock out mutation in hygromycin resistance
Tissue: whole plant
Additional Organism Information:
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:0.830926
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-ratio1.200746
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.785338
Spike_AFFX-r2-Bs-dap_5_signal178.010529
NoiseAvg:2.31,Std:0.09,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_signal56.422768
#P14741
Spike_AFFX-r2-Bs-phe_M_signal78.034225
Corner-Avg:11780,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal131.533173
Spike_AFFX-r2-Ec-bioB_3_signal100.537834
Spike_AFFX-r2-Bs-lys_M_signal35.529331
Spike_AFFX-r2-P1-cre_3_signal5074.153809
Spike_AFFX-r2-Bs-lys_3-5-ratio2.090901
Spike_AFFX-r2-Bs-dap_M_signal525.519897
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.959030
Spike_AFFX-r2-Ec-bioB_avg-signal96.128029
Spike_AFFX-r2-Bs-thr_avg-signal185.053604
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal869.732727
Spike_AFFX-r2-Bs-phe_5_signal60.166035
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1332.906372
RawQ2.254821
Spike_AFFX-r2-Bs-lys_5_signal41.024296
Signal(A)5.179373
%A33.529156
Signal(All)144.199432
Corner+Avg:84,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal308.529633
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal167.232437
Spike_AFFX-r2-Ec-bioD_avg-signal1101.319580
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.625168
Spike_AFFX-r2-Bs-lys_avg-signal54.110458
Spike_AFFX-r2-P1-cre_avg-signal4649.993652
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.845682
Spike_AFFX-r2-Bs-thr_3_signal336.224945
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-signal101.810905
Spike_AFFX-r2-Bs-dap_3_signal735.925903
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.532547
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal294.393707
#M421
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal85.777756
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.048017
Spike_AFFX-r2-Bs-thr_M_signal162.513077
Signal(P)219.900925
Spike_AFFX-r2-Bs-phe_3-5-ratio2.779516
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10569,Count:9
Spike_AFFX-r2-P1-cre_5_signal4225.833496
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7648
Signal(M)19.044693
BackgroundAvg:52.61,Std:0.49,Min:51.4,Max:54.1
Spike_AFFX-r2-Ec-bioC_avg-signal301.461670
Spike_AFFX-r2-Bs-dap_avg-signal479.818756
Spike_AFFX-r2-Bs-dap_3-5-ratio4.134171
Spike_AFFX-r2-Ec-bioB_5_signal56.313068
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.830926
NF1.000000
HZ4
Tau0.015000

Slide: Baubec_616-2_tetraploid-lineC-S2_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 ("Baubec_616-2_tetraploid-lineC-S2_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: Baubec_616-2_tetraploid-lineC-S2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C4S2
Stock Code:
Age: 17
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 21°C.
Percentage Agrose8
Plant Spacing50/plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumOwn medium: MS macro 50ml B5 micro 1ml ammonium iron citrate 50mg sucrose 10g MES 350mg 8% Agar 450ml
Lighting(Source: Fluorescent manufactured by Phillips. Intensity: 105µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: knock out mutation in hygromycin resistance
Tissue: whole plant
Additional Organism Information:
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:0.516625
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-ratio1.326757
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.362439
Spike_AFFX-r2-Bs-dap_5_signal195.707336
NoiseAvg:2.60,Std:0.10,Min:2.3,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_signal48.294170
#P15428
Spike_AFFX-r2-Bs-phe_M_signal83.688110
Corner-Avg:13828,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal100.599846
Spike_AFFX-r2-Ec-bioB_3_signal82.662247
Spike_AFFX-r2-Bs-lys_M_signal38.602737
Spike_AFFX-r2-P1-cre_3_signal4804.071289
Spike_AFFX-r2-Bs-lys_3-5-ratio2.026175
Spike_AFFX-r2-Bs-dap_M_signal522.735779
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.315861
Spike_AFFX-r2-Ec-bioB_avg-signal81.311455
Spike_AFFX-r2-Bs-thr_avg-signal169.386917
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal779.517761
Spike_AFFX-r2-Bs-phe_5_signal69.847832
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1345.502930
RawQ2.282997
Spike_AFFX-r2-Bs-lys_5_signal38.803932
Signal(A)3.680984
%A30.635687
Signal(All)141.983536
Corner+Avg:107,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal235.822998
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal226.477127
Spike_AFFX-r2-Ec-bioD_avg-signal1062.510376
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.637001
Spike_AFFX-r2-Bs-lys_avg-signal52.010082
Spike_AFFX-r2-P1-cre_avg-signal4212.491211
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.727313
Spike_AFFX-r2-Bs-thr_3_signal305.019257
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-signal126.671021
Spike_AFFX-r2-Bs-dap_3_signal840.859863
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.726071
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal262.971985
#M394
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal78.623581
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.896761
Spike_AFFX-r2-Bs-thr_M_signal154.847305
Signal(P)207.913727
Spike_AFFX-r2-Bs-phe_3-5-ratio3.242436
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11837,Count:9
Spike_AFFX-r2-P1-cre_5_signal3620.911621
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6988
Signal(M)13.271144
BackgroundAvg:56.61,Std:0.40,Min:55.2,Max:57.7
Spike_AFFX-r2-Ec-bioC_avg-signal249.397491
Spike_AFFX-r2-Bs-dap_avg-signal519.767639
Spike_AFFX-r2-Bs-dap_3-5-ratio4.296517
Spike_AFFX-r2-Ec-bioB_5_signal60.672272
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.516625
NF1.000000
HZ4
Tau0.015000

Slide: Baubec_616-3_tetraploid-lineC-S2_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baubec_616-3_tetraploid-lineC-S2_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baubec_616-3_tetraploid-lineC-S2_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C4S2
Stock Code:
Age: 17
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 21°C.
Percentage Agrose8
Plant Spacing50/plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumOwn medium: MS macro 50ml B5 micro 1ml ammonium iron citrate 50mg sucrose 10g MES 350mg 8% Agar 450ml
Lighting(Source: Fluorescent manufactured by Phillips. Intensity: 105µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: knock out mutation in hygromycin resistance
Tissue: whole plant
Additional Organism Information:
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:0.490746
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-ratio1.160941
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.546789
Spike_AFFX-r2-Bs-dap_5_signal127.377060
NoiseAvg:2.78,Std:0.11,Min:2.4,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_signal36.495892
#P15303
Spike_AFFX-r2-Bs-phe_M_signal59.224659
Corner-Avg:13996,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.827492
Spike_AFFX-r2-Ec-bioB_3_signal90.561356
Spike_AFFX-r2-Bs-lys_M_signal22.972000
Spike_AFFX-r2-P1-cre_3_signal4359.884766
Spike_AFFX-r2-Bs-lys_3-5-ratio2.235862
Spike_AFFX-r2-Bs-dap_M_signal392.574066
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.146533
Spike_AFFX-r2-Ec-bioB_avg-signal79.978943
Spike_AFFX-r2-Bs-thr_avg-signal136.026794
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal818.349609
Spike_AFFX-r2-Bs-phe_5_signal65.164406
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1315.336548
RawQ2.454710
Spike_AFFX-r2-Bs-lys_5_signal26.186041
Signal(A)3.612700
%A31.249453
Signal(All)141.646561
Corner+Avg:113,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal234.083115
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal150.431839
Spike_AFFX-r2-Ec-bioD_avg-signal1066.843018
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.088997
Spike_AFFX-r2-Bs-lys_avg-signal35.902138
Spike_AFFX-r2-P1-cre_avg-signal4057.679688
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.661552
Spike_AFFX-r2-Bs-thr_3_signal260.819092
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-signal91.606964
Spike_AFFX-r2-Bs-dap_3_signal628.756592
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.607304
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal270.971191
#M379
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal58.548367
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.863867
Spike_AFFX-r2-Bs-thr_M_signal110.765404
Signal(P)209.099243
Spike_AFFX-r2-Bs-phe_3-5-ratio2.308497
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11286,Count:9
Spike_AFFX-r2-P1-cre_5_signal3755.474365
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7128
Signal(M)14.144796
BackgroundAvg:59.35,Std:0.41,Min:57.7,Max:60.6
Spike_AFFX-r2-Ec-bioC_avg-signal252.527161
Spike_AFFX-r2-Bs-dap_avg-signal382.902588
Spike_AFFX-r2-Bs-dap_3-5-ratio4.936184
Spike_AFFX-r2-Ec-bioB_5_signal58.547977
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.490746
NF1.000000
HZ4
Tau0.015000

Slide: Baubec_616-4_tetraploid-lineC-R_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 ("Baubec_616-4_tetraploid-lineC-R_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: Baubec_616-4_tetraploid-lineC-R_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C4R
Stock Code:
Age: 17
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 21°C.
Percentage Agrose8
Plant Spacing50/plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumOwn medium: MS macro 50ml B5 micro 1ml ammonium iron citrate 50mg sucrose 10g MES 350mg 8% Agar 450ml
Lighting(Source: Fluorescent manufactured by Phillips. Intensity: 105µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: knock out mutation in hygromycin resistance
Tissue: whole plant
Additional Organism Information:
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:0.60429
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-ratio1.264604
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.517673
Spike_AFFX-r2-Bs-dap_5_signal165.421906
NoiseAvg:2.49,Std:0.11,Min:2.2,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_signal42.092358
#P15180
Spike_AFFX-r2-Bs-phe_M_signal59.147968
Corner-Avg:14236,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal100.118454
Spike_AFFX-r2-Ec-bioB_3_signal90.148689
Spike_AFFX-r2-Bs-lys_M_signal26.042440
Spike_AFFX-r2-P1-cre_3_signal5706.154297
Spike_AFFX-r2-Bs-lys_3-5-ratio1.914340
Spike_AFFX-r2-Bs-dap_M_signal444.232117
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.224459
Spike_AFFX-r2-Ec-bioB_avg-signal83.222153
Spike_AFFX-r2-Bs-thr_avg-signal145.986130
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal925.241028
Spike_AFFX-r2-Bs-phe_5_signal56.616261
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1545.818726
RawQ2.224210
Spike_AFFX-r2-Bs-lys_5_signal34.743507
Signal(A)4.250617
%A31.600176
Signal(All)146.471313
Corner+Avg:115,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal264.048584
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal162.314026
Spike_AFFX-r2-Ec-bioD_avg-signal1235.529907
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.549759
Spike_AFFX-r2-Bs-lys_avg-signal42.432278
Spike_AFFX-r2-P1-cre_avg-signal5109.179688
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.850066
Spike_AFFX-r2-Bs-thr_3_signal262.002167
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-signal92.692749
Spike_AFFX-r2-Bs-dap_3_signal747.564331
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.670720
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal280.543762
#M422
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal66.510887
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.941203
Spike_AFFX-r2-Bs-thr_M_signal133.863876
Signal(P)217.626633
Spike_AFFX-r2-Bs-phe_3-5-ratio2.866915
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11101,Count:9
Spike_AFFX-r2-P1-cre_5_signal4512.205566
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7208
Signal(M)16.113874
BackgroundAvg:54.06,Std:1.00,Min:52.2,Max:57.3
Spike_AFFX-r2-Ec-bioC_avg-signal272.296173
Spike_AFFX-r2-Bs-dap_avg-signal452.406097
Spike_AFFX-r2-Bs-dap_3-5-ratio4.519137
Spike_AFFX-r2-Ec-bioB_5_signal59.399303
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.604290
NF1.000000
HZ4
Tau0.015000

Slide: Baubec_616-5_tetraploid-lineC-R_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 ("Baubec_616-5_tetraploid-lineC-R_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: Baubec_616-5_tetraploid-lineC-R_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C4R
Stock Code:
Age: 17
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 21°C.
Percentage Agrose8
Plant Spacing50/plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumOwn medium: MS macro 50ml B5 micro 1ml ammonium iron citrate 50mg sucrose 10g MES 350mg 8% Agar 450ml
Lighting(Source: Fluorescent manufactured by Phillips. Intensity: 105µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: knock out mutation in hygromycin resistance
Tissue: whole plant
Additional Organism Information:
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:0.52487
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-ratio1.201526
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.118032
Spike_AFFX-r2-Bs-dap_5_signal117.776680
NoiseAvg:2.58,Std:0.10,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_signal28.304050
#P15346
Spike_AFFX-r2-Bs-phe_M_signal41.841892
Corner-Avg:13798,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal95.915985
Spike_AFFX-r2-Ec-bioB_3_signal83.868423
Spike_AFFX-r2-Bs-lys_M_signal22.544222
Spike_AFFX-r2-P1-cre_3_signal5028.177734
Spike_AFFX-r2-Bs-lys_3-5-ratio2.087106
Spike_AFFX-r2-Bs-dap_M_signal372.729034
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.511778
Spike_AFFX-r2-Ec-bioB_avg-signal84.932915
Spike_AFFX-r2-Bs-thr_avg-signal95.139435
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal884.841858
Spike_AFFX-r2-Bs-phe_5_signal54.675949
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1384.900513
RawQ2.368102
Spike_AFFX-r2-Bs-lys_5_signal27.339819
Signal(A)3.522740
%A31.161772
Signal(All)142.958374
Corner+Avg:107,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal275.333862
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal104.583435
Spike_AFFX-r2-Ec-bioD_avg-signal1134.871216
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.277512
Spike_AFFX-r2-Bs-lys_avg-signal35.648380
Spike_AFFX-r2-P1-cre_avg-signal4606.501953
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.560719
Spike_AFFX-r2-Bs-thr_3_signal156.005646
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-signal67.033760
Spike_AFFX-r2-Bs-dap_3_signal553.977051
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.565139
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.331589
#M356
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.061100
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.150428
Spike_AFFX-r2-Bs-thr_M_signal101.108612
Signal(P)210.526306
Spike_AFFX-r2-Bs-phe_3-5-ratio1.912787
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11226,Count:9
Spike_AFFX-r2-P1-cre_5_signal4184.826660
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7108
Signal(M)14.337397
BackgroundAvg:57.04,Std:1.62,Min:54.2,Max:60.9
Spike_AFFX-r2-Ec-bioC_avg-signal257.332733
Spike_AFFX-r2-Bs-dap_avg-signal348.160919
Spike_AFFX-r2-Bs-dap_3-5-ratio4.703622
Spike_AFFX-r2-Ec-bioB_5_signal75.014328
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.524870
NF1.000000
HZ4
Tau0.015000

Slide: Baubec_616-6_tetraploid-lineC-R_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baubec_616-6_tetraploid-lineC-R_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baubec_616-6_tetraploid-lineC-R_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C4R
Stock Code:
Age: 17
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 21°C.
Percentage Agrose8
Plant Spacing50/plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumOwn medium: MS macro 50ml B5 micro 1ml ammonium iron citrate 50mg sucrose 10g MES 350mg 8% Agar 450ml
Lighting(Source: Fluorescent manufactured by Phillips. Intensity: 105µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.04
Genetic Variation: knock out mutation in hygromycin resistance
Tissue: whole plant
Additional Organism Information:
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:0.727444
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-ratio1.293887
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.445661
Spike_AFFX-r2-Bs-dap_5_signal134.882309
NoiseAvg:2.33,Std:0.07,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_signal36.169651
#P14919
Spike_AFFX-r2-Bs-phe_M_signal56.705120
Corner-Avg:13148,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal126.129616
Spike_AFFX-r2-Ec-bioB_3_signal96.406044
Spike_AFFX-r2-Bs-lys_M_signal23.404495
Spike_AFFX-r2-P1-cre_3_signal5501.714355
Spike_AFFX-r2-Bs-lys_3-5-ratio1.773858
Spike_AFFX-r2-Bs-dap_M_signal397.201874
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.809133
Spike_AFFX-r2-Ec-bioB_avg-signal96.407372
Spike_AFFX-r2-Bs-thr_avg-signal156.518036
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal876.960938
Spike_AFFX-r2-Bs-phe_5_signal60.734074
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1598.393555
RawQ2.103971
Spike_AFFX-r2-Bs-lys_5_signal33.879707
Signal(A)4.698678
%A32.678650
Signal(All)144.451187
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal304.685974
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal167.570480
Spike_AFFX-r2-Ec-bioD_avg-signal1237.677246
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.405525
Spike_AFFX-r2-Bs-lys_avg-signal39.127338
Spike_AFFX-r2-P1-cre_avg-signal4876.898438
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.915826
Spike_AFFX-r2-Bs-thr_3_signal282.453613
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-signal95.003227
Spike_AFFX-r2-Bs-dap_3_signal640.895203
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.822651
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal294.479034
#M437
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.097805
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.034661
Spike_AFFX-r2-Bs-thr_M_signal150.930862
Signal(P)217.991837
Spike_AFFX-r2-Bs-phe_3-5-ratio2.759085
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10888,Count:9
Spike_AFFX-r2-P1-cre_5_signal4252.082031
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7454
Signal(M)17.591444
BackgroundAvg:50.02,Std:0.69,Min:48.7,Max:51.7
Spike_AFFX-r2-Ec-bioC_avg-signal299.582520
Spike_AFFX-r2-Bs-dap_avg-signal390.993134
Spike_AFFX-r2-Bs-dap_3-5-ratio4.751514
Spike_AFFX-r2-Ec-bioB_5_signal66.686462
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.727444
NF1.000000
HZ4
Tau0.015000


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