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Sample GSM159178 Query DataSets for GSM159178
Status Public on May 17, 2007
Title Root, 7-day-old Seedling, biological rep 2
Sample type RNA
 
Source name 7-day-old light-grown rice seedlings
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.
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 Root of 7-day-old light-grown rice seedlings
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 105.2 P 0.000972
AFFX-BioB-M_at 117.2 P 0.00006
AFFX-BioB-3_at 97 P 0.00006
AFFX-BioC-5_at 298.3 P 0.000044
AFFX-BioC-3_at 277.4 P 0.000044
AFFX-BioDn-5_at 607.2 P 0.000044
AFFX-BioDn-3_at 1298.2 P 0.000044
AFFX-CreX-5_at 3334.6 P 0.000044
AFFX-CreX-3_at 4575.5 P 0.000044
AFFX-DapX-5_at 102.4 P 0.000052
AFFX-DapX-M_at 313.7 P 0.000095
AFFX-DapX-3_at 606.1 P 0.000052
AFFX-LysX-5_at 23.1 P 0.000297
AFFX-LysX-M_at 42.4 A 0.0727
AFFX-LysX-3_at 81.2 P 0.00007
AFFX-PheX-5_at 29.8 P 0.000581
AFFX-PheX-M_at 39 P 0.001796
AFFX-PheX-3_at 45.2 P 0.000044
AFFX-ThrX-5_at 39.3 P 0.000509
AFFX-ThrX-M_at 79.6 P 0.000052

Total number of rows: 57381

Table truncated, full table size 1929 Kbytes.




Supplementary file Size Download File type/resource
GSM159178.CEL.gz 4.6 Mb (ftp)(http) CEL

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