Genome characterization of the selected long- and short-sleep mouse lines

• DOI: 10.1007/s00335-016-9663-6
• Publication Date: 2016-09-20T08:47:04Z
• Authors: Robin Dowell; Aaron Odell; Phillip Richmond; Daniel Malmer; Eitan Halper-Stro...; Beth Bennett; Colin Larson; Sonia Leach; Richard A. Radcliffe
• Keywords: Indel; Inbred strain; Human genetics

The Inbred Long- and Short-Sleep (ILS, ISS) mouse lines were selected for differences in acute ethanol sensitivity using the loss of righting response (LORR) as selection trait. show an over tenfold difference LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect genetic underpinnings sensitivity. Here we sequenced genomes ILS ISS investigate DNA variants that contribute their difference. We identified ~2.7 million high-confidence SNPs small indels ~7000 structural between lines; found occur 6382 annotated genes. Using hidden Markov model, able reconstruct genome-wide ancestry patterns eight progenitor strains which derived, quantitative trait loci mapped slightly enriched variants. Finally, by mapping quantifying RNA-seq reads strain-specific rather than reference genome, substantial improvement differential expression analysis lines. This work will help identifying characterizing sequence also aid accurate quantification data generated LXS RIs.