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Experiment: Transcriptome analysis of DELAY OF GERMINATION1 (DOG1) mutant during seed maturation

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-614

Seed dormancy controls the start of a plant's life cycle by preventing germination of a viable seed in an unfavorable season. The molecular mechanisms controlling seed dormancy are not well understood. DELAY OF GERMINATION 1 (DOG1) has been identified as a major Quantitative Trait Locus (QTL) for seed dormancy in a Recombinant Inbred Line (RIL) population between the lowly dormant accession Landsberg erecta (Ler) and the high dormant accession Cape Verde Islands (Cvi) (Alonso Blanco et al., 2003). DOG1 is a key regulator of seed dormancy because dog1 mutants are completely non-dormant and do not show any obvious pleiotropic phenotypes, apart from a reduced seed longevity (Bentsink et al., 2006). We compared the transcriptome of dog1-1 mutant with that of its wild-type background NIL DOG1_Cvi on siliques at mid-maturation phase when DOG1 is highly expressed. This analysis shows the influence of DOG1 on gene expression related to dormancy induction during seed maturation.

About the Experimenter

Name:Dr. Kazumi Nakabayashi
Head of Lab Name:Dr. Wim Soppe
Lab:
Address:Max Planck Institute for Plant Breedinf Research
Carl-von-Linne-Weg 10
Cologne
Postcode: 50829
Country: Germany
 

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

About this Experiment

Experiment Type: genetic_modification_design
Number of Slides:4
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Nakabayashi: Transcriptome analysis of DELAY OF GERMINATION1 (DOG1) mutant during seed maturation

Slide: Nakabayashi_614-4_mutant_Rep2_ATH1

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

Summary Information

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

  • Extract 1 ("Nakabayashi_614-4_mutant_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: Nakabayashi_614-4_mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: dog1-1
Stock Code:
Growth Conditions:
StratificationSeeds are imbibed on filter paper moistened with demineralized water, incubated at 4C for 2 days.
ProtocolFully after-ripened seeds were imbibed on a filter paper moistened with water, incubated at 4C for 2 days, transferred on soil and grown in a growth chamber with constant light at 22ºC with a relative humidity around 60 %. Bolting/flowering started nearly the same time in both genotypes. In this condition, seeds were matured fully at 15 days after pollination.
Plant Spacing4 plants in 9 x 9 cm square pot
wateronce everyday
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in At5g45830
Tissue: siliques
Additional Organism Information:
Sample DescriptionIn the growth condition described above, bolting/flowering started nearly the same time in both genotypes, and seeds were matured fully at 15 days after pollination. Siliques were harvested after 12-13 days after pollination.
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:1.695605
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-ratio1.009784
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.550048
Spike_AFFX-r2-Bs-dap_5_signal539.184021
NoiseAvg:1.72,Std:0.07,Min:1.6,Max:1.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal274.554657
#P12907
Spike_AFFX-r2-Bs-phe_M_signal242.175125
Corner-Avg:4490,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal239.437164
Spike_AFFX-r2-Ec-bioB_3_signal221.505753
Spike_AFFX-r2-Bs-lys_M_signal96.240471
Spike_AFFX-r2-P1-cre_3_signal9373.483398
Spike_AFFX-r2-Bs-lys_3-5-ratio1.886608
Spike_AFFX-r2-Bs-dap_M_signal943.546997
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.095856
Spike_AFFX-r2-Ec-bioB_avg-signal201.281815
Spike_AFFX-r2-Bs-thr_avg-signal571.202087
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2485.496094
Spike_AFFX-r2-Bs-phe_5_signal164.871078
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2792.957031
RawQ1.997168
Spike_AFFX-r2-Bs-lys_5_signal61.846024
Signal(A)8.748247
%A41.174923
Signal(All)154.918213
Corner+Avg:38,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal1045.493652
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal326.079163
Spike_AFFX-r2-Ec-bioD_avg-signal2639.226563
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.584831
Spike_AFFX-r2-Bs-lys_avg-signal91.588562
Spike_AFFX-r2-P1-cre_avg-signal9328.072266
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.240246
Spike_AFFX-r2-Bs-thr_3_signal849.981812
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-signal244.375122
Spike_AFFX-r2-Bs-dap_3_signal1677.851929
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.123702
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal871.411987
#M511
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal116.679176
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.199770
Spike_AFFX-r2-Bs-thr_M_signal589.069763
Signal(P)266.148041
Spike_AFFX-r2-Bs-phe_3-5-ratio1.977783
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3162,Count:9
Spike_AFFX-r2-P1-cre_5_signal9282.662109
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9392
Signal(M)31.992535
BackgroundAvg:63.79,Std:1.20,Min:62.2,Max:68.6
Spike_AFFX-r2-Ec-bioC_avg-signal958.452820
Spike_AFFX-r2-Bs-dap_avg-signal1053.527710
Spike_AFFX-r2-Bs-dap_3-5-ratio3.111835
Spike_AFFX-r2-Ec-bioB_5_signal142.902527
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.695605
NF1.000000
HZ4
Tau0.015000

Slide: Nakabayashi_614-1_background_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 ("Nakabayashi_614-1_background_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: Nakabayashi_614-1_background_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: NIL DOG1_Cvi
Stock Code:
Genetic Background: LerXCvi
Growth Conditions:
StratificationSeeds are imbibed on filter paper moistened with demineralized water, incubated at 4C for 2 days.
ProtocolFully after-ripened seeds were imbibed on a filter paper moistened with water, incubated at 4C for 2 days, transferred on soil and grown in a growth chamber with constant light at 22ºC with a relative humidity around 60 %. Bolting/flowering started nearly the same time in both genotypes. In this condition, seeds were matured fully at 15 days after pollination.
Plant Spacing4 plants in 9 x 9 cm square pot
wateronce everyday
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: NIL DOG1_Cvi is derived from LCN 5-11 (N717127), which has an identical genotype of Ler, apart from an approximately 4.5 Mb Cvi introgression at the bottom of chromosome 5 including the DOG1 gene.
Tissue: siliques
Additional Organism Information:
Sample DescriptionIn the growth condition described above, bolting/flowering started nearly the same time in both genotypes, and seeds were matured fully at 15 days after pollination. Siliques were harvested after 12-13 days after pollination.
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:1.358379
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-ratio1.003554
Spike_AFFX-r2-Ec-bioB_3-5-ratio2.110004
Spike_AFFX-r2-Bs-dap_5_signal633.872070
NoiseAvg:1.77,Std:0.06,Min:1.6,Max:2.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal254.197540
#P12995
Spike_AFFX-r2-Bs-phe_M_signal228.930786
Corner-Avg:4804,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal249.595581
Spike_AFFX-r2-Ec-bioB_3_signal256.187164
Spike_AFFX-r2-Bs-lys_M_signal85.293617
Spike_AFFX-r2-P1-cre_3_signal9648.707031
Spike_AFFX-r2-Bs-lys_3-5-ratio1.479326
Spike_AFFX-r2-Bs-dap_M_signal967.828308
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.154566
Spike_AFFX-r2-Ec-bioB_avg-signal209.066086
Spike_AFFX-r2-Bs-thr_avg-signal514.115906
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2795.645508
Spike_AFFX-r2-Bs-phe_5_signal157.192108
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal3081.744385
RawQ1.911405
Spike_AFFX-r2-Bs-lys_5_signal68.333618
Signal(A)8.144632
%A40.872425
Signal(All)155.230896
Corner+Avg:37,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal1151.662842
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal324.022491
Spike_AFFX-r2-Ec-bioD_avg-signal2938.694824
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.970627
Spike_AFFX-r2-Bs-lys_avg-signal84.904991
Spike_AFFX-r2-P1-cre_avg-signal9631.625000
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.156949
Spike_AFFX-r2-Bs-thr_3_signal801.882996
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-signal236.715134
Spike_AFFX-r2-Bs-dap_3_signal1852.742310
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.102337
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal936.827576
#M492
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal101.087723
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.229322
Spike_AFFX-r2-Bs-thr_M_signal486.267181
Signal(P)265.406647
Spike_AFFX-r2-Bs-phe_3-5-ratio2.061315
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4041,Count:9
Spike_AFFX-r2-P1-cre_5_signal9614.541992
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9323
Signal(M)32.368397
BackgroundAvg:63.51,Std:0.72,Min:62.6,Max:65.8
Spike_AFFX-r2-Ec-bioC_avg-signal1044.245239
Spike_AFFX-r2-Bs-dap_avg-signal1151.480835
Spike_AFFX-r2-Bs-dap_3-5-ratio2.922896
Spike_AFFX-r2-Ec-bioB_5_signal121.415489
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.358379
NF1.000000
HZ4
Tau0.015000

Slide: Nakabayashi_614-2_background_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 ("Nakabayashi_614-2_background_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: Nakabayashi_614-2_background_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: NIL DOG1_Cvi
Stock Code:
Genetic Background: LerXCvi
Growth Conditions:
StratificationSeeds are imbibed on filter paper moistened with demineralized water, incubated at 4C for 2 days.
ProtocolFully after-ripened seeds were imbibed on a filter paper moistened with water, incubated at 4C for 2 days, transferred on soil and grown in a growth chamber with constant light at 22ºC with a relative humidity around 60 %. Bolting/flowering started nearly the same time in both genotypes. In this condition, seeds were matured fully at 15 days after pollination.
Plant Spacing4 plants in 9 x 9 cm square pot
wateronce everyday
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: NIL DOG1_Cvi is derived from LCN 5-11 (N717127), which has an identical genotype of Ler, apart from an approximately 4.5 Mb Cvi introgression at the bottom of chromosome 5 including the DOG1 gene.
Tissue: siliques
Additional Organism Information:
Sample DescriptionIn the growth condition described above, bolting/flowering started nearly the same time in both genotypes, and seeds were matured fully at 15 days after pollination. Siliques were harvested after 12-13 days after pollination.
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:1.481777
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-ratio0.988650
Spike_AFFX-r2-Ec-bioB_3-5-ratio2.961972
Spike_AFFX-r2-Bs-dap_5_signal638.059448
NoiseAvg:1.74,Std:0.04,Min:1.6,Max:1.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal329.293091
#P13096
Spike_AFFX-r2-Bs-phe_M_signal192.989914
Corner-Avg:4864,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal195.356979
Spike_AFFX-r2-Ec-bioB_3_signal237.298370
Spike_AFFX-r2-Bs-lys_M_signal82.149048
Spike_AFFX-r2-P1-cre_3_signal8401.541016
Spike_AFFX-r2-Bs-lys_3-5-ratio1.715525
Spike_AFFX-r2-Bs-dap_M_signal914.418152
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.958783
Spike_AFFX-r2-Ec-bioB_avg-signal170.923447
Spike_AFFX-r2-Bs-thr_avg-signal533.017395
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2136.652344
Spike_AFFX-r2-Bs-phe_5_signal136.922775
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2378.540039
RawQ2.013232
Spike_AFFX-r2-Bs-lys_5_signal64.973442
Signal(A)7.854198
%A40.320034
Signal(All)154.249634
Corner+Avg:35,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal944.262695
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal230.750931
Spike_AFFX-r2-Ec-bioD_avg-signal2257.596191
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.413414
Spike_AFFX-r2-Bs-lys_avg-signal86.195343
Spike_AFFX-r2-P1-cre_avg-signal8449.769531
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.266550
Spike_AFFX-r2-Bs-thr_3_signal645.013855
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-signal186.887878
Spike_AFFX-r2-Bs-dap_3_signal1441.856323
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.113209
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal720.261230
#M517
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal111.463539
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.311000
Spike_AFFX-r2-Bs-thr_M_signal624.745117
Signal(P)261.945984
Spike_AFFX-r2-Bs-phe_3-5-ratio1.685263
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4331,Count:9
Spike_AFFX-r2-P1-cre_5_signal8497.997070
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9197
Signal(M)30.472702
BackgroundAvg:63.77,Std:0.40,Min:63.2,Max:65.0
Spike_AFFX-r2-Ec-bioC_avg-signal832.261963
Spike_AFFX-r2-Bs-dap_avg-signal998.111328
Spike_AFFX-r2-Bs-dap_3-5-ratio2.259752
Spike_AFFX-r2-Ec-bioB_5_signal80.114998
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.481777
NF1.000000
HZ4
Tau0.015000

Slide: Nakabayashi_614-3_mutant_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Nakabayashi_614-3_mutant_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: Nakabayashi_614-3_mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: dog1-1
Stock Code:
Growth Conditions:
StratificationSeeds are imbibed on filter paper moistened with demineralized water, incubated at 4C for 2 days.
ProtocolFully after-ripened seeds were imbibed on a filter paper moistened with water, incubated at 4C for 2 days, transferred on soil and grown in a growth chamber with constant light at 22ºC with a relative humidity around 60 %. Bolting/flowering started nearly the same time in both genotypes. In this condition, seeds were matured fully at 15 days after pollination.
Plant Spacing4 plants in 9 x 9 cm square pot
wateronce everyday
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in At5g45830
Tissue: siliques
Additional Organism Information:
Sample DescriptionIn the growth condition described above, bolting/flowering started nearly the same time in both genotypes, and seeds were matured fully at 15 days after pollination. Siliques were harvested after 12-13 days after pollination.
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:1.121986
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-ratio0.933857
Spike_AFFX-r2-Ec-bioB_3-5-ratio2.079200
Spike_AFFX-r2-Bs-dap_5_signal925.186768
NoiseAvg:2.01,Std:0.06,Min:1.8,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal504.309296
#P13338
Spike_AFFX-r2-Bs-phe_M_signal309.725494
Corner-Avg:5254,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal238.425537
Spike_AFFX-r2-Ec-bioB_3_signal212.270554
Spike_AFFX-r2-Bs-lys_M_signal127.108116
Spike_AFFX-r2-P1-cre_3_signal7896.742188
Spike_AFFX-r2-Bs-lys_3-5-ratio1.233430
Spike_AFFX-r2-Bs-dap_M_signal1422.532959
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.876055
Spike_AFFX-r2-Ec-bioB_avg-signal184.262833
Spike_AFFX-r2-Bs-thr_avg-signal833.734314
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2136.555176
Spike_AFFX-r2-Bs-phe_5_signal232.389801
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2740.637939
RawQ1.980523
Spike_AFFX-r2-Bs-lys_5_signal101.434311
Signal(A)7.828740
%A39.158264
Signal(All)151.142365
Corner+Avg:42,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal1009.753967
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal415.305695
Spike_AFFX-r2-Ec-bioD_avg-signal2438.596680
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.474354
Spike_AFFX-r2-Bs-lys_avg-signal117.884865
Spike_AFFX-r2-P1-cre_avg-signal8176.398438
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.367383
Spike_AFFX-r2-Bs-thr_3_signal946.112183
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-signal319.140350
Spike_AFFX-r2-Bs-dap_3_signal2289.146973
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.282737
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal736.266602
#M540
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal125.112152
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.371451
Spike_AFFX-r2-Bs-thr_M_signal1050.781494
Signal(P)252.178101
Spike_AFFX-r2-Bs-phe_3-5-ratio1.787108
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4764,Count:9
Spike_AFFX-r2-P1-cre_5_signal8456.054688
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8932
Signal(M)26.073524
BackgroundAvg:68.90,Std:0.58,Min:67.8,Max:70.6
Spike_AFFX-r2-Ec-bioC_avg-signal873.010254
Spike_AFFX-r2-Bs-dap_avg-signal1545.622192
Spike_AFFX-r2-Bs-dap_3-5-ratio2.474254
Spike_AFFX-r2-Ec-bioB_5_signal102.092430
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.121986
NF1.000000
HZ4
Tau0.015000


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