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Sample GSM359912 Query DataSets for GSM359912
Status Public on Jul 16, 2009
Title IR29 root, salt-treated, biological replicate 3
Sample type RNA
Source name root, IR29, salt-treated
Organism Oryza sativa Indica Group
Characteristics salt-intolerant
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 IR29 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 8.002868382
AFFX-BioB-5_at 7.947983696
AFFX-BioB-M_at 7.83064936
AFFX-BioC-3_at 9.131914845
AFFX-BioC-5_at 9.156256895
AFFX-BioDn-3_at 11.57390981
AFFX-BioDn-5_at 10.32067455
AFFX-CreX-3_at 13.48229769
AFFX-CreX-5_at 12.99171884
AFFX-DapX-3_at 9.546230072
AFFX-DapX-5_at 7.40266102
AFFX-DapX-M_at 8.732000661
AFFX-LysX-3_at 6.958598215
AFFX-LysX-5_at 5.009830645
AFFX-LysX-M_at 5.272875954
AFFX-Mgr-actin-3_at 5.467099841
AFFX-Mgr-actin-5_at 6.796235747
AFFX-Mgr-actin-M_at 6.063268471
AFFX-Mgr-ef1a-3_at 6.69812321
AFFX-Mgr-ef1a-3_x_at 5.616611262

Total number of rows: 57381

Table truncated, full table size 1729 Kbytes.

Supplementary file Size Download File type/resource
GSM359912.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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