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Sample GSM359914 Query DataSets for GSM359914
Status Public on Jul 16, 2009
Title IR63731 root, control, biological replicate 2
Sample type RNA
Source name root, IR63731, control
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 IR63731 control
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 7.93499984
AFFX-BioB-5_at 7.922351103
AFFX-BioB-M_at 7.759455394
AFFX-BioC-3_at 9.188177223
AFFX-BioC-5_at 9.137155963
AFFX-BioDn-3_at 11.55162395
AFFX-BioDn-5_at 10.09144821
AFFX-CreX-3_at 13.3018703
AFFX-CreX-5_at 12.8069956
AFFX-DapX-3_at 10.27007526
AFFX-DapX-5_at 8.088630272
AFFX-DapX-M_at 9.36644695
AFFX-LysX-3_at 7.516123874
AFFX-LysX-5_at 5.557469431
AFFX-LysX-M_at 6.080898712
AFFX-Mgr-actin-3_at 5.211062182
AFFX-Mgr-actin-5_at 6.688309828
AFFX-Mgr-actin-M_at 5.981392636
AFFX-Mgr-ef1a-3_at 5.894290671
AFFX-Mgr-ef1a-3_x_at 5.422925494

Total number of rows: 57381

Table truncated, full table size 1729 Kbytes.

Supplementary file Size Download File type/resource
GSM359914.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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