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Sample GSM195221 Query DataSets for GSM195221
Status Public on Jun 30, 2007
Title Ovary 1, biological rep 1
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 were 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 416 P 0.000754
AFFX-BioB-M_at 516.1 P 0.000052
AFFX-BioB-3_at 353.3 P 0.000044
AFFX-BioC-5_at 776.7 P 0.000052
AFFX-BioC-3_at 776.7 P 0.000044
AFFX-BioDn-5_at 2947.8 P 0.000044
AFFX-BioDn-3_at 6938.8 P 0.000052
AFFX-CreX-5_at 16756.1 P 0.000052
AFFX-CreX-3_at 19878.6 P 0.000044
AFFX-DapX-5_at 423.3 P 0.000052
AFFX-DapX-M_at 1099.5 P 0.000195
AFFX-DapX-3_at 1854.6 P 0.000052
AFFX-LysX-5_at 74.7 P 0.000081
AFFX-LysX-M_at 183.3 P 0.036569
AFFX-LysX-3_at 598.2 P 0.000081
AFFX-PheX-5_at 100.3 P 0.000445
AFFX-PheX-M_at 143.7 P 0.000662
AFFX-PheX-3_at 227.8 P 0.00141
AFFX-ThrX-5_at 72.9 P 0.046482
AFFX-ThrX-M_at 190.8 P 0.000052

Total number of rows: 57381

Table truncated, full table size 1960 Kbytes.

Supplementary file Size Download File type/resource
GSM195221.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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