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Series GSE16341 Query DataSets for GSE16341
Status Public on Jun 01, 2010
Title A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression array: Transcript and Genome Hybridizations
Platform organism Oryza sativa
Sample organisms Oryza sativa Indica Group; Oryza sativa Japonica Group
Experiment type Expression profiling by array
Genome variation profiling by array
Summary The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.
 
Overall design Total RNA from 3-4 week shoots and genomic DNA both Nipponbare and 93-11 were analyzed.
 
Contributor(s) Horiuchi Y, Harushima Y, Kurata N
Citation(s) 20482895
Submission date May 29, 2009
Last update date Dec 27, 2017
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
 
Platforms (1)
GPL2025 [Rice] Affymetrix Rice Genome Array
Samples (27)
GSM409771 Nipponbare_shoot 3-4weeks, biological rep1
GSM409772 Nipponbare_shoot 3-4weeks, biological rep2
GSM409773 Nipponbare_shoot 3-4weeks, biological rep3
Relations
BioProject PRJNA115273

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16341_RAW.tar 155.4 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
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