Genome characterization of the selected long- and short-sleep mouse lines.
Genome characterization of the selected long- and short-sleep mouse lines.
复制标题
选定的长和短睡小鼠系的基因组表征。
DOI：
10.1007/s00335-016-9663-6
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发表时间：
2016-12
期刊：
影响因子：
2.5
通讯作者：
Radcliffe, Richard A.
中科院分区：
文献类型：
--
作者：
Dowell, Robin;Odell, Aaron;Richmond, Phillip;Malmer, Daniel;Halper-Stromberg, Eitan;Bennett, Beth;Larson, Colin;Leach, Sonia;Radcliffe, Richard A.
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 the selection trait. The lines show an over tenfold difference in LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect the genetic underpinnings of acute ethanol sensitivity. Here we have sequenced the genomes of the ILS and ISS to investigate the DNA variants that contribute to their sensitivity difference. We identified ~2.7 million high-confidence SNPs and small indels and ~7000 structural variants between the lines; variants were found to occur in 6382 annotated genes. Using a hidden Markov model, we were able to reconstruct the genome-wide ancestry patterns of the eight inbred progenitor strains from which the ILS and ISS were derived, and found that quantitative trait loci that have been mapped for LORR were slightly enriched for DNA variants. Finally, by mapping and quantifying RNA-seq reads from the ILS and ISS to their strain-specific genomes rather than to the reference genome, we found a substantial improvement in a differential expression analysis between the lines. This work will help in identifying and characterizing the DNA sequence variants that contribute to the difference in ethanol sensitivity between the ILS and ISS and will also aid in accurate quantification of RNA-seq data generated from the LXS RIs. The online version of this article (doi:10.1007/s00335-016-9663-6) contains supplementary material, which is available to authorized users.
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DOI：
10.1111/gbb.12018
发表时间：
2013-03
期刊：
Genes, brain, and behavior
影响因子：
--
作者：
Darlington TM;Ehringer MA;Larson C;Phang TL;Radcliffe RA
通讯作者：
Radcliffe RA
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
DOI：
10.1111/acer.12678
发表时间：
2015-04
期刊：
Alcoholism, clinical and experimental research
影响因子：
--
作者：
Bennett B;Larson C;Richmond PA;Odell AT;Saba LM;Tabakoff B;Dowell R;Radcliffe RA
通讯作者：
Radcliffe RA
DOI：
10.1111/j.1530-0277.1989.tb00310.x
发表时间：
1989-04-01
期刊：
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
影响因子：
--
作者：
DEFRIES, JC;WILSON, JR;PETERSEN, DR
通讯作者：
PETERSEN, DR
影响因子：
30.8
作者：
Chesler, EJ;Lu, L;Williams, RW
通讯作者：
Williams, RW