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Sample GSM159216 Query DataSets for GSM159216
Status Public on May 17, 2007
Title Seed (S4, 11 - 20 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 [11 - 20 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
E-mail(s) kapoors@genomeindia.org
Phone 91 11 65171135
URL http://www.dpmb.ac.in/
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 38.8 P 0.001593
AFFX-BioB-M_at 37.6 P 0.001796
AFFX-BioB-3_at 53.7 P 0.000081
AFFX-BioC-5_at 110 P 0.000044
AFFX-BioC-3_at 156.5 P 0.000052
AFFX-BioDn-5_at 233.6 P 0.000044
AFFX-BioDn-3_at 649.3 P 0.000052
AFFX-CreX-5_at 1575.7 P 0.000044
AFFX-CreX-3_at 2167.5 P 0.000044
AFFX-DapX-5_at 115.9 P 0.000052
AFFX-DapX-M_at 388.7 P 0.000052
AFFX-DapX-3_at 952.9 P 0.000044
AFFX-LysX-5_at 22.9 P 0.000195
AFFX-LysX-M_at 37.4 P 0.003595
AFFX-LysX-3_at 140.2 P 0.000081
AFFX-PheX-5_at 42.4 P 0.000044
AFFX-PheX-M_at 67.3 P 0.000509
AFFX-PheX-3_at 59.7 P 0.000127
AFFX-ThrX-5_at 31.8 P 0.000095
AFFX-ThrX-M_at 79.8 P 0.000052

Total number of rows: 57381

Table truncated, full table size 1907 Kbytes.




Supplementary file Size Download File type/resource
GSM159216.CEL.gz 4.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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