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Sample GSM195228 Query DataSets for GSM195228
Status Public on Jun 30, 2007
Title Embryo
Sample type RNA
 
Source name Rice 10-day-old embryo
Organism Oryza sativa
Characteristics genotype: Japonica Nipponbare
age: Rice 10-day-old embryo after pollination
age: Rice 10-day-old embryo after pollination
Growth protocol Rice were grown in season beginning from May to October, in the experimental farm of the Institute of Genetics and Developmental biology, Beijing.
Extracted molecule total RNA
Extraction protocol remove lemma and palea,embryos were dissected from grains 10 days after flowering
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
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 692.8 P 0.000754
AFFX-BioB-M_at 574.4 P 0.000147
AFFX-BioB-3_at 485.9 P 0.000044
AFFX-BioC-5_at 1517.9 P 0.000044
AFFX-BioC-3_at 1979.8 P 0.000044
AFFX-BioDn-5_at 3684.6 P 0.000044
AFFX-BioDn-3_at 7141.3 P 0.000044
AFFX-CreX-5_at 17734 P 0.000052
AFFX-CreX-3_at 19207.2 P 0.000044
AFFX-DapX-5_at 1921.7 P 0.000044
AFFX-DapX-M_at 3230.5 P 0.000081
AFFX-DapX-3_at 4163.8 P 0.000044
AFFX-LysX-5_at 209.5 P 0.000044
AFFX-LysX-M_at 325.7 P 0.001796
AFFX-LysX-3_at 810.1 P 0.000044
AFFX-PheX-5_at 455.7 P 0.000044
AFFX-PheX-M_at 376.8 P 0.000044
AFFX-PheX-3_at 446.6 P 0.000044
AFFX-ThrX-5_at 469 P 0.00007
AFFX-ThrX-M_at 721.2 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1959 Kbytes.




Supplementary file Size Download File type/resource
GSM195228.CEL.gz 4.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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