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Sample GSM359913 Query DataSets for GSM359913
Status Public on Jul 16, 2009
Title IR63731 root, control, biological replicate 1
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
E-mail(s) ute.baumann@adelaide.edu.au
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
ID_REF
VALUE log2 signal intensity (RMA)

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.917769965
AFFX-BioB-5_at 8.06813452
AFFX-BioB-M_at 7.716602679
AFFX-BioC-3_at 9.150261016
AFFX-BioC-5_at 9.145575769
AFFX-BioDn-3_at 11.58064393
AFFX-BioDn-5_at 10.22092227
AFFX-CreX-3_at 13.34614892
AFFX-CreX-5_at 12.89373024
AFFX-DapX-3_at 10.41652864
AFFX-DapX-5_at 8.268342793
AFFX-DapX-M_at 9.496168771
AFFX-LysX-3_at 7.66016633
AFFX-LysX-5_at 5.745585491
AFFX-LysX-M_at 6.062389888
AFFX-Mgr-actin-3_at 5.467099841
AFFX-Mgr-actin-5_at 6.564181461
AFFX-Mgr-actin-M_at 5.844611198
AFFX-Mgr-ef1a-3_at 6.028686615
AFFX-Mgr-ef1a-3_x_at 5.324348888

Total number of rows: 57381

Table truncated, full table size 1728 Kbytes.




Supplementary file Size Download File type/resource
GSM359913.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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