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Sample GSM393522 Query DataSets for GSM393522
Status Public on Jun 02, 2009
Title wild type, biological rep2
Sample type RNA
 
Source name Wild type
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: vegetative part
age: stage 1.03
genotype: WT
Growth protocol plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C
Extracted molecule total RNA
Extraction protocol RNeasy 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 Wild type, vegetative part of seedlings at stage 1.03
Data processing Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). An alternative CDF (tinesath1cdf) was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007; http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html)
 
Submission date Apr 17, 2009
Last update date Jun 02, 2009
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 GPL8455
Series (2)
GSE15722 Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana, expression data
GSE15726 Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana

Data table header descriptions
ID_REF
VALUE Absolute expression values log2 transformed in the RMA procedure

Data table
ID_REF VALUE
AT1G01010 4.287958175
AT1G01030 4.446506652
AT1G01040 7.13558015
AT1G01050 9.921873005
AT1G01060 7.113570231
AT1G01070 5.557883514
AT1G01080 9.5362415
AT1G01090 11.73048319
AT1G01100 11.74250263
AT1G01110 4.424572868
AT1G01120 9.799151816
AT1G01130 4.739461948
AT1G01140 8.966942158
AT1G01150 3.33240199
AT1G01160 7.447405021
AT1G01170 10.72558619
AT1G01180 4.079233563
AT1G01190 4.765037844
AT1G01200 4.387012058
AT1G01220 7.721870249

Total number of rows: 20777

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM393522.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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