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Sample GSM159184 Query DataSets for GSM159184
Status Public on May 17, 2007
Title Y Leaf, biological rep 2
Sample type RNA
Source name Mature 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 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 Y Leaf (leaf subtending the shoot apical meristem) from mature 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 105.2 P 0.00039
AFFX-BioB-M_at 122.7 P 0.000044
AFFX-BioB-3_at 114 P 0.000044
AFFX-BioC-5_at 340 P 0.000044
AFFX-BioC-3_at 316.3 P 0.000044
AFFX-BioDn-5_at 711.8 P 0.000044
AFFX-BioDn-3_at 1263.3 P 0.000052
AFFX-CreX-5_at 3592.8 P 0.000044
AFFX-CreX-3_at 4675.3 P 0.000044
AFFX-DapX-5_at 398.7 P 0.000044
AFFX-DapX-M_at 741.1 P 0.000052
AFFX-DapX-3_at 1150.6 P 0.000044
AFFX-LysX-5_at 56 P 0.000044
AFFX-LysX-M_at 96.9 P 0.000297
AFFX-LysX-3_at 200.1 P 0.000052
AFFX-PheX-5_at 73.8 P 0.000044
AFFX-PheX-M_at 119.8 P 0.000044
AFFX-PheX-3_at 121.5 P 0.000044
AFFX-ThrX-5_at 123.8 P 0.00007
AFFX-ThrX-M_at 176.6 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1920 Kbytes.

Supplementary file Size Download File type/resource
GSM159184.CEL.gz 4.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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