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Sample GSM409434 Query DataSets for GSM409434
Status Public on Jun 09, 2009
Title 9311_young panicle 2cm, biological rep5
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
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 207.972 P 0.000661624
AFFX-BioB-M_at 221.761 P 4.42873e-05
AFFX-BioB-3_at 165.067 P 4.42873e-05
AFFX-BioC-5_at 498.751 P 4.42873e-05
AFFX-BioC-3_at 629.871 P 4.42873e-05
AFFX-BioDn-5_at 1079.58 P 4.42873e-05
AFFX-BioDn-3_at 2643.53 P 4.42873e-05
AFFX-CreX-5_at 6086.95 P 5.16732e-05
AFFX-CreX-3_at 7880.76 P 4.42873e-05
AFFX-DapX-5_at 26.9538 P 0.00687065
AFFX-DapX-M_at 192.561 P 0.000753643
AFFX-DapX-3_at 452.766 P 6.02111e-05
AFFX-LysX-5_at 26.7057 P 9.4506e-05
AFFX-LysX-M_at 56.4931 M 0.0629293
AFFX-LysX-3_at 179.956 P 0.00010954
AFFX-PheX-5_at 19.2353 P 0.00499819
AFFX-PheX-M_at 41.7884 P 0.0103112
AFFX-PheX-3_at 71.1281 P 0.000224668
AFFX-ThrX-5_at 5.39541 A 0.51489
AFFX-ThrX-M_at 40.8261 P 0.000296708

Total number of rows: 57381

Table truncated, full table size 2175 Kbytes.




Supplementary file Size Download File type/resource
GSM409434.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM409434.CHP.gz 312.8 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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