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Sample GSM159188 Query DataSets for GSM159188
Status Public on May 17, 2007
Title SAM, biological rep 3
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
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 110.8 P 0.000225
AFFX-BioB-M_at 132.3 P 0.000044
AFFX-BioB-3_at 102.9 P 0.000044
AFFX-BioC-5_at 315.2 P 0.000044
AFFX-BioC-3_at 349.7 P 0.000044
AFFX-BioDn-5_at 662.3 P 0.000044
AFFX-BioDn-3_at 1279.1 P 0.000044
AFFX-CreX-5_at 3504.5 P 0.000052
AFFX-CreX-3_at 4349.4 P 0.000044
AFFX-DapX-5_at 116.5 P 0.000081
AFFX-DapX-M_at 258.8 P 0.000127
AFFX-DapX-3_at 392 P 0.000052
AFFX-LysX-5_at 20.2 P 0.000044
AFFX-LysX-M_at 43.8 A 0.0727
AFFX-LysX-3_at 101.3 P 0.000052
AFFX-PheX-5_at 29.1 P 0.000195
AFFX-PheX-M_at 34.8 P 0.000052
AFFX-PheX-3_at 49.1 P 0.000044
AFFX-ThrX-5_at 17 P 0.002275
AFFX-ThrX-M_at 63.2 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1924 Kbytes.




Supplementary file Size Download File type/resource
GSM159188.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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