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Sample GSM195222 Query DataSets for GSM195222
Status Public on Jun 30, 2007
Title Ovary 2, biological rep 2
Sample type RNA
Source name mature ovary
Organism Oryza sativa
Characteristics genotype: Japonica Nipponbare
age: ovaries at anthesis
age: rice ovary before pollination
Growth protocol natural conditions,growing season begins from December to next April, in an experimental farm in Hainan, China.
Extracted molecule total RNA
Extraction protocol remove lemma and palea from floret, the stigma is extracted from pistil, the remainder of the pistil containing the style is used as the ovary samples.
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 31, 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 420.3 P 0.000857
AFFX-BioB-M_at 467.3 P 0.000052
AFFX-BioB-3_at 342.9 P 0.000052
AFFX-BioC-5_at 730.4 P 0.00006
AFFX-BioC-3_at 690.1 P 0.000044
AFFX-BioDn-5_at 2715.8 P 0.000044
AFFX-BioDn-3_at 6344.2 P 0.000052
AFFX-CreX-5_at 16137.7 P 0.000044
AFFX-CreX-3_at 18589.9 P 0.000044
AFFX-DapX-5_at 547.3 P 0.000052
AFFX-DapX-M_at 1322.9 P 0.000127
AFFX-DapX-3_at 2113.8 P 0.000052
AFFX-LysX-5_at 112.7 P 0.000127
AFFX-LysX-M_at 209.1 P 0.00844
AFFX-LysX-3_at 619.7 P 0.000044
AFFX-PheX-5_at 104.8 P 0.000972
AFFX-PheX-M_at 187.9 P 0.000509
AFFX-PheX-3_at 267.6 P 0.000581
AFFX-ThrX-5_at 138.3 P 0.003595
AFFX-ThrX-M_at 227.6 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1958 Kbytes.

Supplementary file Size Download File type/resource
GSM195222.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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