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Sample GSM159220 Query DataSets for GSM159220
Status Public on May 17, 2007
Title Seed (S5, 21 - 29 dap), biological rep 2
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 [21 - 29 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 113.6 P 0.002867
AFFX-BioB-M_at 116.9 P 0.000127
AFFX-BioB-3_at 134 P 0.000052
AFFX-BioC-5_at 292 P 0.000052
AFFX-BioC-3_at 399.9 P 0.000044
AFFX-BioDn-5_at 635.5 P 0.000044
AFFX-BioDn-3_at 1384.4 P 0.00006
AFFX-CreX-5_at 4297.6 P 0.000044
AFFX-CreX-3_at 4878 P 0.000044
AFFX-DapX-5_at 218.5 P 0.000044
AFFX-DapX-M_at 807.4 P 0.000052
AFFX-DapX-3_at 2013.6 P 0.000044
AFFX-LysX-5_at 80.1 P 0.000044
AFFX-LysX-M_at 71.7 P 0.000754
AFFX-LysX-3_at 332.1 P 0.000052
AFFX-PheX-5_at 96.7 P 0.000044
AFFX-PheX-M_at 160.6 P 0.00007
AFFX-PheX-3_at 115.6 P 0.000052
AFFX-ThrX-5_at 65.3 P 0.00011
AFFX-ThrX-M_at 170.1 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1916 Kbytes.

Supplementary file Size Download File type/resource
GSM159220.CEL.gz 4.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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