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Sample GSM195218 Query DataSets for GSM195218
Status Public on Jun 30, 2007
Title stigma 1, biological rep1
Sample type RNA
 
Source name mature stigmas
Organism Oryza sativa
Characteristics genotype: Japonica Nipponbare
age: unpollinated stigmas at anthesis
age: rice stigma 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 collected by cutting the pistil just below the base of the plumose stigma
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
E-mail(s) wyxu@genetics.ac.cn
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
ID_REF
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 396.3 P 0.000754
AFFX-BioB-M_at 479.2 P 0.00007
AFFX-BioB-3_at 282.5 P 0.00006
AFFX-BioC-5_at 610.4 P 0.000052
AFFX-BioC-3_at 674.2 P 0.000044
AFFX-BioDn-5_at 2571.6 P 0.000044
AFFX-BioDn-3_at 5740.8 P 0.000052
AFFX-CreX-5_at 14884.8 P 0.000052
AFFX-CreX-3_at 18222.6 P 0.000044
AFFX-DapX-5_at 352.7 P 0.000127
AFFX-DapX-M_at 874.6 P 0.000446
AFFX-DapX-3_at 1356.6 P 0.00006
AFFX-LysX-5_at 75.3 P 0.000195
AFFX-LysX-M_at 142.4 A 0.0727
AFFX-LysX-3_at 335.6 P 0.000095
AFFX-PheX-5_at 96.1 P 0.002275
AFFX-PheX-M_at 169.4 P 0.000297
AFFX-PheX-3_at 179.2 P 0.002867
AFFX-ThrX-5_at 63 P 0.033677
AFFX-ThrX-M_at 131.9 P 0.000147

Total number of rows: 57381

Table truncated, full table size 1958 Kbytes.




Supplementary file Size Download File type/resource
GSM195218.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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