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Sample GSM195226 Query DataSets for GSM195226
Status Public on Jun 30, 2007
Title Root
Sample type RNA
Source name Rice root
Organism Oryza sativa
Characteristics genotype: Japonica Nipponbare
age: two-week old rice root
age: two-week old rice root
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 seedling root 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 371.7 P 0.001796
AFFX-BioB-M_at 331.7 P 0.000127
AFFX-BioB-3_at 283.8 P 0.000127
AFFX-BioC-5_at 1059.1 P 0.000052
AFFX-BioC-3_at 921.9 P 0.000044
AFFX-BioDn-5_at 1826.8 P 0.000044
AFFX-BioDn-3_at 5108.2 P 0.000052
AFFX-CreX-5_at 9900 P 0.000052
AFFX-CreX-3_at 12804 P 0.000044
AFFX-DapX-5_at 1374.8 P 0.000044
AFFX-DapX-M_at 2236.2 P 0.000095
AFFX-DapX-3_at 3044.6 P 0.000052
AFFX-LysX-5_at 137.4 P 0.00006
AFFX-LysX-M_at 264.9 P 0.028457
AFFX-LysX-3_at 490.1 P 0.00007
AFFX-PheX-5_at 255.6 P 0.003212
AFFX-PheX-M_at 176.6 P 0.001796
AFFX-PheX-3_at 331.6 P 0.000052
AFFX-ThrX-5_at 339.5 P 0.000109
AFFX-ThrX-M_at 420.5 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1963 Kbytes.

Supplementary file Size Download File type/resource
GSM195226.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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