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Sample GSM393555 Query DataSets for GSM393555
Status Public on Jun 02, 2009
Title gra2-D
Sample type genomic
 
Channel 1
Source name gra2-D DNA tiling
Organism Arabidopsis thaliana
Characteristics tissue: rosette
Growth protocol plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C
Extracted molecule genomic DNA
Extraction protocol DNeasy plant mini kit (Qiagen) , according to manufacturer protocol
Label biotin
Label protocol Standard affymetrix protocol
 
Channel 2
Source name WT
Organism Arabidopsis thaliana
Characteristics tissue: rosette
Growth protocol plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C
Extracted molecule genomic DNA
Extraction protocol DNeasy plant mini kit (Qiagen) , according to manufacturer protocol
Label biotin
Label protocol Standard affymetrix protocol
 
 
Hybridization protocol Standard affymetrix protocol
Scan protocol Standard affymetrix protocol
Description grandifolia2-D DNA tiling array
Data processing The algorithm MAT (Model based Analysis of Tiling-arrays (http://liulab.dfci.harvard.edu/MAT/) was used in order to detect duplicated or deleted genomic regions.
bar-file: binary file containing the MAT score for each probe. bed-file: text file containing the enriched genomics regions
 
Submission date Apr 17, 2009
Last update date Sep 24, 2010
Contact name Nathalie Gonzalez
E-mail(s) nagon@psb.vib-ugent.be
Phone +32 (0)9 331 39 56
Organization name VIB
Department Plant System Biology
Lab System Biology of Yield
Street address Technologiepark 927
City Gent
ZIP/Postal code 9052
Country Belgium
 
Platform ID GPL10977
Series (2)
GSE15725 Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana, tiling array data
GSE15726 Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana

Supplementary file Size Download File type/resource
GSM393555_WT.CEL.gz 24.8 Mb (ftp)(http) CEL
GSM393555_WT_versus_gra2-D.bed.gz 9.3 Kb (ftp)(http) BED
GSM393555_gra2-D.CEL.gz 26.0 Mb (ftp)(http) CEL
GSM393555_gra2-D.bar.gz 20.9 Mb (ftp)(http) BAR
Processed data provided as supplementary file

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