GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM429983 Query DataSets for GSM429983
Status Public on Jul 22, 2009
Title Rice mutant phoenix (pho) panicle rep1
Sample type RNA
Source name rice mutant phoenix (pho) panicle Rep1
Organism Oryza sativa
Characteristics genotype: Oryza sativa L. ssp. Indica, mutant phoenix (pho)
tissue: rice panicle (5cm-8cm)
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 degee 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 (5cm-8cm) 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 345.5 P 0.004017
AFFX-BioB-M_at 400.8 P 0.000052
AFFX-BioB-3_at 274.9 P 0.000169
AFFX-BioC-5_at 764.7 P 0.000052
AFFX-BioC-3_at 829.3 P 0.000044
AFFX-BioDn-5_at 1995.1 P 0.000044
AFFX-BioDn-3_at 5085 P 0.000052
AFFX-CreX-5_at 11299.1 P 0.000052
AFFX-CreX-3_at 15031.7 P 0.000044
AFFX-DapX-5_at 950.2 P 0.000044
AFFX-DapX-M_at 1696.7 P 0.000081
AFFX-DapX-3_at 2463.1 P 0.000052
AFFX-LysX-5_at 120.9 P 0.000052
AFFX-LysX-M_at 203 P 0.005565
AFFX-LysX-3_at 643.5 P 0.000052
AFFX-PheX-5_at 227.2 P 0.00007
AFFX-PheX-M_at 311.9 P 0.000044
AFFX-PheX-3_at 365.9 P 0.000509
AFFX-ThrX-5_at 222.4 P 0.000095
AFFX-ThrX-M_at 349.2 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1957 Kbytes.

Supplementary file Size Download File type/resource
GSM429983.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap