Diversity Outcross (DO) QTL Mapping data - high fat diet, multiple phenotypes

Description 

A panel of 150 Diversity Outbred (DO) mice were phenotyped over a period of 24 weeks. 100 of the mice received a chow diet and 50 received a high fat diet from weaning until sacrifice. The mice were genotyped at 7,854 SNPs on the Mouse Universal Genotyping Array (MUGA) and quantitative trait locus (QTL) mapping was performed on the phenotypes. Animals were subject to a battery of noninvasive physiological measurements to obtain clinical parameters, including: serum cholesterol (at 8 and 24 weeks), early and late measurements of clinical plasma chemistries (lipids, glucose, insulin) and body composition (weight, percent fat, lean tissue mass). Coat color was also recorded. The genotypes were reconstructed using a hidden Markov model that produced genotype probabilities for each sample at each SNP. These were then condensed down to eight founder allele dosages that were used to map each trait. Mapping was carried out with QTLRel, which accounts for the complex genetic relationships between mice.

Data

Phenotype Data

This file includes all of the phenotype measurements for the 150 DO mice. It is a tabular, comma separated file with column names.
Churchill.Mamm.Gen.2012.phenotypes.csv

Array Genotype Data

• Genotyping quality summary for each sample 30nov2010_DNAReport.csv
• Allele intensity file for all samples in this batch 30nov2010_FinalReport.txt
• Genotyping quality summary for each SNP 30nov2010_LocusSummary.csv
• Genotyping quality summary for each sample and SNP 30nov2010_LocusXDNA.csv
• Listing of each sample ID and location Sample_Map.txt
• Listing of each SNP and its location SNP_Map.txt 
• Genotyping quality summary for each sample 27Jan2011_DNAReport.csv
• Allele intensity file for all samples in this batch 27Jan2011_FinalReport.txt
• Genotyping quality summary for each SNP 27Jan2011_LocusSummary.csv
• Genotyping quality summary for each sample and SNP 27Jan2011_LocusXDNA.csv
• Listing of each sample ID and location Sample_Map.txt
• Listing of each SNP and its location SNP_Map.txt 
• Genotyping quality summary for each sample 17mar2011_DNAReport.csv
• Allele intensity file for all samples in this batch 17mar2011_FinalReport.txt
• Genotyping quality summary for each SNP 17mar2011_LocusSummary.csv
• Genotyping quality summary for each sample and SNP 17mar2011_LocusXDNA.csv
• Listing of each sample ID and location Sample_Map.txt
• Listing of each SNP and its location SNP_Map.txt

Reconstructed Genotype Data for Svenson et al. Genetics 2012

Folder of reconstructed genotype files from hidden Markov model ([MF]##.genotype.probs.txt). genotypeprobs.zip319 MB

Reconstructed Genotype Data for Churchill et al. Mammalian Genome 2012

This zip file contains 143 files, one for each sample that could be genotyped. 7 samples were not genotyped due to technical reasons. Each file is a tabular, comma separated file with 36 columns and 7,854 rows. Each column represents one unphased genotype. Each row represents a single SNP. Each cell contains the posterior probability that the sample contains the genotype of that column at the SNP for that row. There is also a “SNP_Map.txt” file that contains the SNP locations. Churchill.Mamm.Gen.2012.genotype.probs.zip

QTL Results for Svenson et al. Genetics 2012

Folder of QTL mapping results for each phenotype (*.QTLRel.LOD.txt) QTLRelLOD.zip25 MB
Maximum QTL location for each phenotype Svenson.et.al.QTL.table.xlsx

QTL Results for Churchill et al. Mammalian Genome 2012

This zip file contains the QTL results. Text files are tab delimited. The LOD scores are in files called *.QTLRel.LOD.txt. The model coefficients are in files called *.QTLRel.coef.txt. The maximum LOD score over 1,000 permutations is in files called *.QTLRel.perms.txt. Each phenotype contains a PDF with a QTL plot and coefficient and effect plots for significant QTL. Churchill.Mamm.Gen.2012.QTL.zip

Publications 

Churchill GA, Gatti DM, Munger SC, Svenson KL
Mamm Genome. 2012 Oct;23(9-10):713-8.    [ Full Text ].     PMCID: PMC3524832

Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA
Genetics. 2012 Feb;190(2):437-47.   [ Full Text ]     PMCID: PMC3276626