DOI: 10.5061/dryad.2rs41
title: Data from: Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice

description: Although mice are the most widely used mammalian model organism, genetic
 studies have suffered from limited mapping resolution due to extensive
 linkage disequilibrium (LD) that is characteristic of crosses among inbred
 strains. Carworth Farms White (CFW) mice are a commercially available
 outbred mouse population that exhibit rapid LD decay in comparison to
 other available mouse populations. We performed a genome-wide association
 study (GWAS) of behavioral, physiological and gene expression phenotypes
 using 1,200 male CFW mice. We used genotyping by sequencing (GBS) to
 obtain genotypes at 92,734 SNPs. We also measured gene expression using
 RNA sequencing in three brain regions. Our study identified numerous
 behavioral, physiological and expression quantitative trait loci (QTLs).
 We integrated the behavioral QTL and eQTL results to implicate specific
 genes, including Azi2 in sensitivity to methamphetamine and Zmynd11 in
 anxiety-like behavior. The combination of CFW mice, GBS and RNA sequencing
 constitutes a powerful approach to GWAS in mice.
description: Physiological and
 behavioral trait dataPhysiological and
 behavioural phenotype data on 1,219 mice from the Carworth Farms White
 (CFW) outbred mouse stock. The data are stored in comma-delimited
 ("csv") format, with one line per sample.pheno.csvSNPs genotyped in CFW miceInformation about 92,734 single nucleotide polymorphisms (SNPs) on chromosomes 1-19 genotyped in the CFW outbred mouse cohort. The table is stored in space-delimited columns, with one row per SNP. All genomic positions are based on Mouse Genome Assembly 38 from the NCBI database (mm10, December 2011).map.txtGenotype data for 1,161 mice at 92,734 SNPsTable with space-delimited columns containing genotype data for 1,161 mice at 92,734 SNPs. The first column ("id") is the sample id, and the second column ("discard") indicates whether the sample should be discarded because of flowcell samples that were mislabeled, and so we cannot be sure of the identity of these samples.geno.txt.gzPLINK sample information fileCFW genotypes stored in PLINK .fam/.bim/.bed format.cfw.famPLINK SNP information fileCFW genotypes stored in PLINK .bed/.bim/.fam format.cfw.bimPLINK binary genotype fileCFW genotypes stored in PLINK .bed/.bim/.fam format.cfw.bedGenotype calls from hippocampus RNA-seq dataVCF file containing the genotypes at SNPs identified from RNA-seq data in the hippocampus. Genotypes and allele counts in this VCF file are used for analyzing allele-specific expression in the hippocampus.rna_HIP.vcfGenotype calls from prefrontal cortex RNA-seq dataVCF file containing the genotypes at SNPs identified from RNA-seq data in the prefrontal cortex. Genotypes and allele counts in this VCF file are used for analyzing allele-specific expression in the prefrontal cortex.rna_PFC.vcfGenotype calls from striatum RNA-seq dataVCF file containing the genotypes at SNPs identified from RNA-seq data in the striatum. Genotypes and allele counts in this VCF file are used for analyzing allele-specific expression in the striatum.rna_STR.vcfNormalized RNA-seq fpkm valuesTab-delimited file containing normalized fpkm values obtained from the RNA-seq experiments in 3 brain tissues, after normalization across samples. The fpkm values for the 3 brain tissues have been combined into a single file. Each row corresponds to a sample, and each column corresponds to a gene. The brain tissue for each measurement is indicated by column header. A suffix of .HIP is added to the gene names for hippocampus measurements, .STR for the striatum, and .PFC for the prefrontal cortex. This file only includes data for genes with mean fpkm &gt; 1 prior to normalization.combined.thr.norm.fpkm