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Series GSE71553 Query DataSets for GSE71553
Status Public on Feb 25, 2016
Title High Density Rice Array (HDRA6.4) developed by the McCouch-Rice Lab at Cornell University
Organism Oryza sativa
Experiment type Genome variation profiling by SNP array
Summary A High Density Rice Array (HDRA) was developed as an Affymetrix Custom GeneChip Array by the McCouch Rice Lab at Cornell University. The HDRA assays 700,000 SNPs, or approximately one SNP every 0.54 Kb across the rice genome (genome size = 380 Mb). It was designed to capture most of the haplotype variation observed in a discovery panel consisting of 16M SNPs (generated by sequencing 125 rice genomes at ~7X genome coverage) and to maximize the inclusion of non-synonymous SNPs. Six probes per SNP target were designed as 3 A-allele and 3 B-allele probes at offsets from center ranging from -6 to +6. A small fraction of SNPs have only 4 probes (2-A, 2-B). For all SNPs, the “A” allele is the reference allele (Os-Nipponbare-Reference-IRGSP-1.0 assembly). Additionally, we designed 23,656 x 25-bp probes complimentary to invariant regions of the genome that were used to normalize systematic differences between samples. An estimated 45% of HDRA SNPs map within genes, hitting all 39,045 unique, non-TE rice gene models (MSUv7 rice genome annotation, GFF3 file, Feb. 7, 2012, http://rice.plantbiology.msu.edu/), while 55% of SNPs map to intergenic regions. Non-synonymous are found in 91% of unique, non-TE gene models, and 57% of genic SNPs are distributed within exons, 36% within introns, 5% within 5’ UTRs and 2% within 3’ UTRs. Of the intergenic SNPs, 40% are located in putative regulatory regions within 2 Kb of a transcriptional start site.
 
Overall design Using the HDRA, SNP variation was assayed in a collection of 1,568 diverse O. stiva accessions and the resulting genotypic dataset was analyzed for population structure and used for Genome Wide Association Studies (GWAS).
 
Contributor(s) Wright MH, Tung C, DeClerck G, Agosto-Pérez F, Harrington SE, Shi Y, Singh N, McNally KL, Ebana K, Yano M, Eizenga G, McClung A, Mezey J, McCouch SR
Citation(s) 26842267
Submission date Jul 30, 2015
Last update date May 26, 2016
Contact name Susan R. McCouch
E-mail srm4@cornell.edu
Phone 607-255-0420
Organization name Cornell University
Department Plant Breeding & Genetics
Lab McCouch RiceLab
Street address 162 Emerson Hall
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
 
Platforms (1)
GPL20755 High Density Rice Array (HDRA) Affymetrix Custom GeneChip Array
Samples (1568)
GSM1836804 High Density Rice Array (HDRAG6.4) NSFTV1
GSM1836805 High Density Rice Array (HDRAG6.4) NSFTV2
GSM1836806 High Density Rice Array (HDRAG6.4) NSFTV3
Relations
BioProject PRJNA291537

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
GSE71553_Matrix.csv.gz 1.2 Gb (ftp)(http) CSV
GSE71553_RAW.tar 40.3 Gb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data is available on Series record

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