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Sample GSM159186 Query DataSets for GSM159186
Status Public on May 17, 2007
Title SAM, biological rep 1
Sample type RNA
Source name Rice plants at floral transition stage
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 Trizol, according to the manufacturer's instructions
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 Shoot apical meristem (SAM, upto 0.5 mm) from rice plants at floral transition stage
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 100.8 P 0.000972
AFFX-BioB-M_at 98 P 0.000052
AFFX-BioB-3_at 82.6 P 0.000052
AFFX-BioC-5_at 249.1 P 0.000044
AFFX-BioC-3_at 274.5 P 0.000044
AFFX-BioDn-5_at 520.8 P 0.000044
AFFX-BioDn-3_at 1120.8 P 0.000052
AFFX-CreX-5_at 2956.1 P 0.000044
AFFX-CreX-3_at 3690.7 P 0.000044
AFFX-DapX-5_at 177.5 P 0.000052
AFFX-DapX-M_at 393.6 P 0.000081
AFFX-DapX-3_at 540.2 P 0.000052
AFFX-LysX-5_at 34.6 P 0.000052
AFFX-LysX-M_at 47.8 P 0.006187
AFFX-LysX-3_at 134.7 P 0.00011
AFFX-PheX-5_at 40.5 P 0.000225
AFFX-PheX-M_at 71.6 P 0.000169
AFFX-PheX-3_at 89.1 P 0.000044
AFFX-ThrX-5_at 41.4 P 0.000127
AFFX-ThrX-M_at 97.5 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1928 Kbytes.

Supplementary file Size Download File type/resource
GSM159186.CEL.gz 4.5 Mb (ftp)(http) CEL

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