GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM195225 Query DataSets for GSM195225
Status Public on Jun 30, 2007
Title Shoot
Sample type RNA
Source name Rice shoot
Organism Oryza sativa
Characteristics genotype: Japonica Nipponbare
age: two-week old rice shoot
age: two-week old rice shoot
Growth protocol Rice (O. sativa L. cv. Nipponbare) seeds were germinated and grown in a growth container for two weeks (28 degree, 16 h light, 8 h dark, photo intensity 240 ¦Ìm photos m-2s-1).
Extracted molecule total RNA
Extraction protocol the shoot were cutted and harvested from two-week seeding
total RNA was isolated and purified by Qiagen RNeasy kit
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from rice stigma
Data processing The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Submission date May 29, 2007
Last update date Jul 29, 2009
Contact name Wenying Xu
Organization name Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences
Street address Datun Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL2025
Series (1)
GSE7951 Genome-wide gene expression profiling of rice stigma

Data table header descriptions
VALUE MAS5-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 'detection p-value', p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 424.5 P 0.000972
AFFX-BioB-M_at 369.7 P 0.000169
AFFX-BioB-3_at 288.8 P 0.000052
AFFX-BioC-5_at 1165.3 P 0.000052
AFFX-BioC-3_at 1301.7 P 0.000044
AFFX-BioDn-5_at 2389.6 P 0.000044
AFFX-BioDn-3_at 6055.2 P 0.000052
AFFX-CreX-5_at 12248.2 P 0.000052
AFFX-CreX-3_at 13772.2 P 0.000044
AFFX-DapX-5_at 1473.5 P 0.000044
AFFX-DapX-M_at 2450.1 P 0.000081
AFFX-DapX-3_at 3054.6 P 0.000052
AFFX-LysX-5_at 134.7 P 0.00007
AFFX-LysX-M_at 251.6 P 0.009337
AFFX-LysX-3_at 528.9 P 0.000052
AFFX-PheX-5_at 269.1 P 0.00011
AFFX-PheX-M_at 241.7 P 0.000258
AFFX-PheX-3_at 286.5 P 0.00034
AFFX-ThrX-5_at 377.5 P 0.000052
AFFX-ThrX-M_at 473.3 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1963 Kbytes.

Supplementary file Size Download File type/resource
GSM195225.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap