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Sample GSM393530 Query DataSets for GSM393530
Status Public on Jun 02, 2009
Title gra3-D, biological rep1
Sample type RNA
 
Source name gra3-D mutant
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: vegetative part
age: stage 1.03
genotype: gra3-D
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 gra3-D mutant, 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 4.171070735
AT1G01030 4.699401135
AT1G01040 7.235519209
AT1G01050 9.701476387
AT1G01060 7.260602831
AT1G01070 5.379172745
AT1G01080 9.352830822
AT1G01090 11.70310066
AT1G01100 11.55156907
AT1G01110 4.694050825
AT1G01120 9.794457243
AT1G01130 4.64113699
AT1G01140 9.119409164
AT1G01150 3.345450299
AT1G01160 7.572477382
AT1G01170 10.60454417
AT1G01180 4.035416318
AT1G01190 4.816857343
AT1G01200 4.627819515
AT1G01220 7.696207552

Total number of rows: 20777

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM393530.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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