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Sample GSM562209 Query DataSets for GSM562209
Status Public on May 05, 2011
Title Control, biological rep2
Sample type RNA
 
Source name Arabidopsis Thaliana control
Organism Arabidopsis thaliana
Characteristics stress: Control
sample type: cell suspension culture
Treatment protocol An incubation of 30 min at high light or 1-h at dark were selected as the optimum time to monitor the changes in the transcription profile in the microarray experiments.
Growth protocol Arabidopsis cell suspension culture was maintained in 200 mL of liquid growth medium (Jouannea and Peaudlen, 1967; Axelos et al., 1992) by gentle agitation at 120 rpm at 24 ºC under continuous illumination (50 microE/m2/s) in an incubator shaker. Cells were sub-cultured with a 1/20 dilution factor every 7 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the acid guanidine isothiocyanate-phenol-chloroform method using Trizol reagent. Total RNA was treated with TURBO DNase to eliminate traces of contaminating genomic DNA.
Label biotin
Label protocol Biotin-labelled cRNA was produced by in vitro transcription using GeneChip® 3' IVT Express Kit. The biotin-labelled cRNA was degraded by alkaline digestion and used for hybridization with ATH1 arrays.
 
Hybridization protocol Technical steps as target hybridization, washing and staining of the arrays were performed sequentially as described in the Affymetrix GeneChip expression analysis technical manual using the Affymetrix once-cycle target labelling and control reagents, an Affymetrix GeneChip hybridization oven 640, and Affymetrix Fluidics Station 450
Scan protocol Microarrays were scanned using Affymetrix GenChip Scanner 3000 7G.
Description Gene expression data from Arabidopsis Thaliana control
Data processing Data was standardized from R using the affy Bioconductor package. Methods: Robust Multi-array Average and quantile normalization.
 
Submission date Jul 01, 2010
Last update date May 05, 2011
Contact name Francisco García García
E-mail(s) fgarcia@cipf.es
Organization name CIPF
Department Bionformatics & Biostatistics Unit
Street address Eduardo Primo Yúfera, 3
City Valencia
ZIP/Postal code 46012
Country Spain
 
Platform ID GPL198
Series (1)
GSE22671 Gene expression from Arabidopsis under high light conditions

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
244901_at 6.598264876
244902_at 7.164557234
244903_at 7.511445217
244904_at 5.85940971
244905_at 3.906055938
244906_at 4.319049943
244907_at 3.815184661
244908_at 3.903272278
244909_at 3.790926906
244910_s_at 3.788639205
244911_at 3.733157148
244912_at 9.576303763
244913_at 4.576483898
244914_at 4.047748885
244915_s_at 4.276615836
244916_at 3.871813175
244917_at 4.113020723
244918_at 3.745439991
244919_at 6.846659529
244920_s_at 8.220606768

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM562209_Control_2.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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