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Sample GSM409422 Query DataSets for GSM409422
Status Public on Jun 09, 2009
Title Nipponbare_young panicle 2cm, biological rep2
Sample type RNA
 
Source name young panicle 2cm
Organism Oryza sativa Japonica Group
Characteristics tissue: young panicle
cultivar: Nipponbare
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 Nov 02, 2010
Contact name Nori Kurata
E-mail(s) nkurata@lab.nig.ac.jp
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
ID_REF
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 369.665 P 0.000258358
AFFX-BioB-M_at 412.799 P 4.42873e-05
AFFX-BioB-3_at 249.991 P 4.42873e-05
AFFX-BioC-5_at 786.685 P 5.16732e-05
AFFX-BioC-3_at 1107.02 P 4.42873e-05
AFFX-BioDn-5_at 1973.31 P 4.42873e-05
AFFX-BioDn-3_at 4927.38 P 4.42873e-05
AFFX-CreX-5_at 10124.8 P 5.16732e-05
AFFX-CreX-3_at 13241.9 P 4.42873e-05
AFFX-DapX-5_at 452.306 P 4.42873e-05
AFFX-DapX-M_at 866.241 P 9.4506e-05
AFFX-DapX-3_at 1252.27 P 5.16732e-05
AFFX-LysX-5_at 64.7183 P 0.000195116
AFFX-LysX-M_at 114.394 A 0.0780018
AFFX-LysX-3_at 299.105 P 4.42873e-05
AFFX-PheX-5_at 71.4853 P 0.000169227
AFFX-PheX-M_at 95.9081 P 0.000258358
AFFX-PheX-3_at 143.935 P 4.42873e-05
AFFX-ThrX-5_at 115.181 P 0.000389797
AFFX-ThrX-M_at 189.884 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2182 Kbytes.




Supplementary file Size Download File type/resource
GSM409422.CEL.gz 5.3 Mb (ftp)(http) CEL
GSM409422.CHP.gz 308.6 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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