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Sample GSM159210 Query DataSets for GSM159210
Status Public on May 17, 2007
Title Seed (S2, 3 - 4 dap), biological rep 1
Sample type RNA
Source name Seed, after pollination from rice plants
Organism Oryza sativa
Characteristics Subspecies: indica, Variety: IR64
Treatment protocol Untreated
Growth protocol Rice seeds were disinfected with 0.1% HgCl2 for 1 h, thoroughly washed with RO (reverse-osmosis) water and soaked overnight in RO water. Seedlings were grown in RO water, at 28±1 degree celsius, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark. After 15 days seedlings were transferred in pots kept in greenhouse
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed using modified guanidine hydrochloride method as described (Jain et al., 2006, Biochem Biophys Res Commun, 345, 646-651)
Label Biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using script EukGE-WS2v5.
Scan protocol GeneChips were scanned using GeneChip Scanner 3000
Description Seed [3 - 4 days after pollination (dap)] from rice plants
Data processing The data were analyzed with GeneChipOperating Software (GCOS 1.2.1) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was arbitrarily set to 100.
Submission date Jan 29, 2007
Last update date May 17, 2007
Contact name Sanjay Kapoor
Phone 91 11 65171135
Organization name University of Delhi South Campus
Department Department of 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)
GSE6893 Expression data for reproductive development in rice

Data table header descriptions
ID_REF Probe set ID
VALUE GCOS 1.2.1 calculated signal intensity
ABS_CALL The call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE p-value indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 72 P 0.000446
AFFX-BioB-M_at 52.1 P 0.00007
AFFX-BioB-3_at 52.1 P 0.000127
AFFX-BioC-5_at 172.6 P 0.000044
AFFX-BioC-3_at 170 P 0.000044
AFFX-BioDn-5_at 377.1 P 0.000044
AFFX-BioDn-3_at 776.2 P 0.000052
AFFX-CreX-5_at 1970.7 P 0.000044
AFFX-CreX-3_at 2687.1 P 0.000044
AFFX-DapX-5_at 40.3 P 0.000052
AFFX-DapX-M_at 272.2 P 0.000052
AFFX-DapX-3_at 857 P 0.000044
AFFX-LysX-5_at 25.2 P 0.000169
AFFX-LysX-M_at 46.8 P 0.001246
AFFX-LysX-3_at 161 P 0.000052
AFFX-PheX-5_at 26.8 P 0.00039
AFFX-PheX-M_at 38.3 P 0.00006
AFFX-PheX-3_at 69.9 P 0.000052
AFFX-ThrX-5_at 7.9 A 0.156732
AFFX-ThrX-M_at 53.2 P 0.00011

Total number of rows: 57381

Table truncated, full table size 1926 Kbytes.

Supplementary file Size Download File type/resource
GSM159210.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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