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Sample GSM359922 Query DataSets for GSM359922
Status Public on Jul 16, 2009
Title Pokkali root, salt-treated, biological replicate 1
Sample type RNA
Source name root, Pokkali, salt-treated
Organism Oryza sativa Indica Group
Characteristics salt-tolerant
Treatment protocol On day 22 after germination, salt treatment commenced by adding NaCl and CaCl2 (5:1 molar concentration) in two steps over a period of 3 days to the nutrient solution reservoir. Salinity in the treatment reservoir reached 7.4 dS/m. Plants were harvested on day 30.
Growth protocol Plants were grown in sand-filled tanks and irrigated with nutrient solution (for details see Walia et al (2005), Plant Physiol. 139:822-35) for 30 days.
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIzol and subsequently purified using an RNeasy spin column (Qiagen) and an on-column DNase treatment.
Label biotin
Label protocol Approx. 8 µg of total RNA was processed to produce biotinylated cRNA targets.
Hybridization protocol Standard Affymetrix procedures.
Scan protocol Standard Affymetrix procedures.
Description Pokkali salt-treated
Data processing The data were normalized using the Robust Multichip Average method of background correction, quantile normalisation, and summarisation of cell signal intensities (Irrizary et al., 2003).
Submission date Jan 13, 2009
Last update date Mar 11, 2009
Contact name Ute Baumann
Phone ++61 8 83037388
Organization name University of Adelaide
Department Australian Centre for Plant Functional Genomics
Street address Hartley Grove
City Glen Osmond
State/province SA
ZIP/Postal code 5064
Country Australia
Platform ID GPL2025
Series (1)
GSE14403 Root-specific transcriptional profiling of contrasting rice genotypes in response to salinity stress

Data table header descriptions
VALUE log2 signal intensity (RMA)

Data table
AFFX-BioB-3_at 7.736506634
AFFX-BioB-5_at 7.690168293
AFFX-BioB-M_at 7.635000578
AFFX-BioC-3_at 8.955908517
AFFX-BioC-5_at 8.944101945
AFFX-BioDn-3_at 11.31073408
AFFX-BioDn-5_at 10.04080191
AFFX-CreX-3_at 13.31531886
AFFX-CreX-5_at 12.81565416
AFFX-DapX-3_at 10.31726829
AFFX-DapX-5_at 8.293951649
AFFX-DapX-M_at 9.529258655
AFFX-LysX-3_at 7.562497445
AFFX-LysX-5_at 5.873629994
AFFX-LysX-M_at 6.132813024
AFFX-Mgr-actin-3_at 5.123976243
AFFX-Mgr-actin-5_at 6.621618494
AFFX-Mgr-actin-M_at 5.754733219
AFFX-Mgr-ef1a-3_at 5.966616095
AFFX-Mgr-ef1a-3_x_at 5.477975482

Total number of rows: 57381

Table truncated, full table size 1728 Kbytes.

Supplementary file Size Download File type/resource
GSM359922.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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