GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM409431 Query DataSets for GSM409431
Status Public on Jun 09, 2009
Title 9311_young panicle 2cm, biological rep2
Sample type RNA
Source name young panicle 2cm
Organism Oryza sativa Indica Group
Characteristics tissue: young panicle
cultivar: 93-11
Extracted molecule total RNA
Extraction protocol total RNA was isolated and purified by RNeasy Plant Mini Kit (QIAGEN)
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol According to Affymetrix standard procedure, 10 micrograms of fragmented cRNA were hybridized to an array for 16-18 hours at 45┬░C with constant rotation at 60 rpm. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station.
Scan protocol GeneChips were scanned using Affymetrix GeneArray 3000 scanner.
Description Gene expression data from rice young panicle
Data processing The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method.
Submission date May 28, 2009
Last update date Jun 08, 2009
Contact name Nori Kurata
Phone +81-55-981-6808
Fax +81-55-981-6879
Organization name National Institute of Genetics
Lab Plant Genetics Lab.
Street address 1111 Yata
City Mishima
ZIP/Postal code 411-8540
Country Japan
Platform ID GPL2025
Series (1)
GSE16265 SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip

Data table header descriptions
VALUE Affymetrix GeneChip® Operating Software (GCOS, Version 1.3, Affymetrix) calculated Signal intensity
ABS_CALL The call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 166.681 P 0.0012475
AFFX-BioB-M_at 142.212 P 7.00668e-05
AFFX-BioB-3_at 78.4331 P 5.16732e-05
AFFX-BioC-5_at 288.452 P 6.02111e-05
AFFX-BioC-3_at 382.232 P 4.42873e-05
AFFX-BioDn-5_at 672.816 P 4.42873e-05
AFFX-BioDn-3_at 1683.15 P 5.16732e-05
AFFX-CreX-5_at 4392.15 P 5.16732e-05
AFFX-CreX-3_at 5833.57 P 4.42873e-05
AFFX-DapX-5_at 220.74 P 4.42873e-05
AFFX-DapX-M_at 497.721 P 9.4506e-05
AFFX-DapX-3_at 656.007 P 5.16732e-05
AFFX-LysX-5_at 27.7957 P 0.000296708
AFFX-LysX-M_at 66.5861 P 0.0200219
AFFX-LysX-3_at 154.111 P 8.14279e-05
AFFX-PheX-5_at 46.7832 P 0.000296708
AFFX-PheX-M_at 51.5516 P 0.00227496
AFFX-PheX-3_at 95.0232 P 4.42873e-05
AFFX-ThrX-5_at 47.6849 P 0.000340305
AFFX-ThrX-M_at 87.6039 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2174 Kbytes.

Supplementary file Size Download File type/resource
GSM409431.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM409431.CHP.gz 313.0 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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