Data from: Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice

Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA

Date Published: July 5, 2016

DOI: http://dx.doi.org/10.5061/dryad.2rs41

 

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Title Physiological and behavioral trait data
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Description Physiological 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.
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Title SNPs genotyped in CFW mice
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Description Information 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).
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Title Genotype data for 1,161 mice at 92,734 SNPs
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Description Table 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.
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Title PLINK sample information file
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Description CFW genotypes stored in PLINK .fam/.bim/.bed format.
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Title PLINK SNP information file
Downloaded 23 times
Description CFW genotypes stored in PLINK .bed/.bim/.fam format.
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Title PLINK binary genotype file
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Description CFW genotypes stored in PLINK .bed/.bim/.fam format.
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Title Genotype calls from hippocampus RNA-seq data
Downloaded 39 times
Description VCF 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.
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Title Genotype calls from prefrontal cortex RNA-seq data
Downloaded 30 times
Description VCF 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.
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Title Genotype calls from striatum RNA-seq data
Downloaded 29 times
Description VCF 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.
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Title Normalized RNA-seq fpkm values
Downloaded 67 times
Description Tab-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 > 1 prior to normalization.
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When using this data, please cite the original publication:

Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA (2016) Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. Nature Genetics 48(8): 919-926. http://dx.doi.org/10.1038/ng.3609

Additionally, please cite the Dryad data package:

Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA (2016) Data from: Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2rs41
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