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Sample GSM387562 Query DataSets for GSM387562
Status Public on Jun 03, 2009
Title Wild-type, biological rep. 1
Sample type RNA
 
Source name 15 days old rice shoot unstressed
Organism Oryza sativa Indica Group
Characteristics cultivar: Pusa Basmati 1
tissue: 15 days old rice shoot
genotype/variation: wildtype
Treatment protocol Untreated seedlings were used for shoot tissue
Growth protocol Seedlings were raised on MS medium without antibiotic selection for 15 days.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 450C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
Scan protocol GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000
Description Gene espression data of 15 days old rice shoot in wild-type plants
Data processing First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using Avadis 4.2 prophetic software (Strandgenomics, Bangalore, India)
 
Submission date Mar 30, 2009
Last update date Jun 03, 2009
Contact name Akhilesh Kumar Tyagi
E-mail(s) akhilesh@genomeindia.org
Phone 91-11-24115095
Fax 91-11-24115095
Organization name University of Delhi South Campus, Benito Juarez Road India
Department Plant Molecular Biology
Street address Benito Juarez Road
City New Delhi
State/province Delhi
ZIP/Postal code 110021
Country India
 
Platform ID GPL2025
Series (1)
GSE15448 Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice

Data table header descriptions
ID_REF
VALUE GCRMA normalised signal values

Data table
ID_REF VALUE
AFFX-BioB-3_at 170.49185
AFFX-BioB-5_at 128.46422
AFFX-BioB-M_at 157.27586
AFFX-BioC-3_at 652.5942
AFFX-BioC-5_at 514.5801
AFFX-BioDn-3_at 3608.5571
AFFX-BioDn-5_at 1707.2506
AFFX-CreX-3_at 16855.945
AFFX-CreX-5_at 16055.239
AFFX-DapX-3_at 1958.7163
AFFX-DapX-5_at 506.8954
AFFX-DapX-M_at 1258.1595
AFFX-LysX-3_at 350.81625
AFFX-LysX-5_at 35.866833
AFFX-LysX-M_at 97.50065
AFFX-Mgr-actin-3_at 4.6992536
AFFX-Mgr-actin-5_at 5.947194
AFFX-Mgr-actin-M_at 3.8546586
AFFX-Mgr-ef1a-3_at 4.550571
AFFX-Mgr-ef1a-3_x_at 4.5537605

Total number of rows: 57381

Table truncated, full table size 1590 Kbytes.




Supplementary file Size Download File type/resource
GSM387562.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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