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Data Set Group: UCSD AIL Advanced Intercross Line (Apr18) RNA-Seq modify this page

Data Set: UCSD AIL Striatum (Apr18) RNA-Seq modify this page
GN Accession: GN845
GEO Series: No Geo series yet
Title: Genome wide association study of behavioral, physiological and gene expression traits in a multigenerational mouse intercross
Organism: Mouse (mm10)
Group: AIL
Tissue: Striatum mRNA
Dataset Status: Public
Platforms: Illumina ScriptSeq RNA-Seq v2
Normalization: RNA-seq
Contact Information
Abraham Palmer
University of California, San Diego
9500 Gilman Drive #0667
La Jolla, CA 92093 USA
Tel. 858-534-2093
aapalmer@ucsd.edu
Website
Download datasets and supplementary data files

Specifics of this Data Set:
Striatum

Summary:

Genome wide association analyses (GWAS) in model organisms have numerous advantages compared to human GWAS, including the ability to use populations with well-defined genetic diversity, the ability to collect tissue for gene expression analysis and the ability to perform experimental manipulations. We examined behavioral, physiological, and gene expression traits in 1,063 male and female mice from a 50-generation intercross between two inbred strains (LG/J and SM/J). We used genotyping by sequencing in conjunction with whole genome sequence data from the two founder strains to obtain genotypes at 4.3 million SNPs. As expected, all alleles were common (mean MAF=0.35) and linkage disequilibrium degraded rapidly, providing excellent power and sub-megabase mapping precision. We identified 126 genome-wide significant loci for 50 traits and integrated this information with 7,081 cis-eQTLs and 1,476 trans-eQTLs identified in hippocampus, striatum and prefrontal cortex. We replicated several loci that were identified using an earlier generation of this intercross, including an association between locomotor activity and a locus containing a single gene, Csmd1. We also showed that Csmd1 mutant mice recapitulated the locomotor phenotype. Our results demonstrate the utility of this population, identify numerous novel associations, and provide examples of replication in an independent cohort, which is customary in human genetics, and replication by experimental manipulation, which is a unique advantage of model organisms.



About the cases used to generate this set of data:


About the tissue used to generate this set of data:


About the array platform:


About data values and data processing:


Notes:


Experiment Type:


Contributor:

Natalia M. Gonzales, Jungkyun Seo, Ana Isabel Hernandez-Cordero, Celine L. St. Pierre, Jennifer S. Gregory, Margaret G. Distler, Mark Abney, Stefan Canzar, Arimantas Lionikas, Abraham A. Palmer



Citation:

Genome wide association study of behavioral, physiological and gene expression traits in a multigenerational mouse intercross



Data source acknowledgment:


Study Id:
272

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GeneNetwork support from:
  • The UT Center for Integrative and Translational Genomics
  • NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
  • NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
  • NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
  • NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
  • NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
  • NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)
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