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Sample GSM195224 Query DataSets for GSM195224
Status Public on Jun 30, 2007
Title Suspension cell
Sample type RNA
Source name Rice suspension cell
Organism Oryza sativa
Characteristics genotype: Japonica Nipponbare
4 weeks suspension cultured cell
Growth protocol Rice calli were cultured in N6 liquid medium containing 2,4-D (1 mg/l) in a rotary shaker at 150 rpm at 25 degree for 4 weeks with the medium refreshed every week.
Extracted molecule total RNA
Extraction protocol the suspension cultured cell were collected by centrifuge
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 429.3 P 0.00141
AFFX-BioB-M_at 407.8 P 0.000147
AFFX-BioB-3_at 336.2 P 0.000052
AFFX-BioC-5_at 970.8 P 0.000052
AFFX-BioC-3_at 1206.7 P 0.000044
AFFX-BioDn-5_at 2523.8 P 0.000044
AFFX-BioDn-3_at 6500.7 P 0.00006
AFFX-CreX-5_at 11521.8 P 0.000052
AFFX-CreX-3_at 14650 P 0.000044
AFFX-DapX-5_at 1086.3 P 0.00007
AFFX-DapX-M_at 1667.7 P 0.000095
AFFX-DapX-3_at 1833.9 P 0.00006
AFFX-LysX-5_at 95.4 P 0.00011
AFFX-LysX-M_at 192.9 P 0.020022
AFFX-LysX-3_at 360 P 0.00007
AFFX-PheX-5_at 224.6 P 0.000147
AFFX-PheX-M_at 156.4 P 0.002023
AFFX-PheX-3_at 185.3 P 0.000754
AFFX-ThrX-5_at 199.7 P 0.000754
AFFX-ThrX-M_at 319.2 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1958 Kbytes.

Supplementary file Size Download File type/resource
GSM195224.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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