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Sample GSM429984 Query DataSets for GSM429984
Status Public on Jul 22, 2009
Title Rice wild-type panicle rep2
Sample type RNA
Source name rice wild-type panicle Rep2
Organism Oryza sativa
Characteristics genotype: Oryza sativa L. ssp. Indica, Zhongxian 3037
tissue: rice panicle (9cm-12cm)
Growth protocol plants were grown in paddy fields in Beijing
Extracted molecule total RNA
Extraction protocol total RNA was isolated by TRIZOL 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 450.
Scan protocol GeneChip was scanned using the Affymetrix GeneChip Scanner
Description the panicle (9cm-12cm) was collected directly
Gene expression data from rice mutant phoenix (pho) panicle
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 Jul 20, 2009
Last update date Aug 06, 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)
GSE17194 Genome-wide gene expression profiling of rice Indica cultivar Zhongxian 3037 and mutant phoenix (pho) panicle

Data table header descriptions
ID_REF Probe set ID
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 454.3 P 0.000754
AFFX-BioB-M_at 454.2 P 0.000052
AFFX-BioB-3_at 400.4 P 0.00006
AFFX-BioC-5_at 1147.4 P 0.000052
AFFX-BioC-3_at 1315.8 P 0.000169
AFFX-BioDn-5_at 2440.1 P 0.000044
AFFX-BioDn-3_at 5918.8 P 0.000044
AFFX-CreX-5_at 16487.6 P 0.000044
AFFX-CreX-3_at 19432.3 P 0.000044
AFFX-DapX-5_at 201.3 P 0.00007
AFFX-DapX-M_at 643.2 P 0.000754
AFFX-DapX-3_at 1299.5 P 0.000052
AFFX-LysX-5_at 48.1 P 0.000753
AFFX-LysX-M_at 161.4 A 0.131361
AFFX-LysX-3_at 231.3 P 0.000052
AFFX-PheX-5_at 66.4 P 0.001796
AFFX-PheX-M_at 54.6 A 0.0727
AFFX-PheX-3_at 159.7 P 0.00006
AFFX-ThrX-5_at 37.7 A 0.275146
AFFX-ThrX-M_at 143.9 P 0.000581

Total number of rows: 57381

Table truncated, full table size 1959 Kbytes.

Supplementary file Size Download File type/resource
GSM429984.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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