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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...a single . Epigenetic modifications have also been shown to vary across47 individuals in humans (McVicker et al., 2013; Kang et al., 2021), rats (Rintisch et al., 2014), cattle48 (Prowse-Wilkins et al., 2022), and mice, including some of the DO/CC founders (Link et al., 2018;49 Schilling et al., 2009; Zhou...
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Resource: The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains
- Toyoyuki Takada,
- Toshinobu Ebata,
- Hideki Noguchi,
- Thomas M. Keane,
- David J. Adams,
- Takanori Narita,
- Tadasu Shin-I,
- Hironori Fujisawa,
- Atsushi Toyoda,
- Kuniya Abe,
- Yuichi Obata,
- Yoshiyuki Sakaki,
- Kazuo Moriwaki,
- Asao Fujiyama,
- Yuji Kohara,
- and Toshihiko Shiroishi
Genome Res. August 2013 23: 1329-1338; Published in Advance April 19, 2013, doi:10.1101/gr.156497.113
.... molossinus and M. m. domesticus, respectively. We also used the sequence of SPRET/EiJ as a reference for Mus spretus and used the rat sequence as an outgroup. The WSB and SPRET/EiJ sequences were obtained from the MGP data set. The genomic regions for which a single B6/MSM topology was supported...
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LETTER: Significant gene content variation characterizes the genomes of inbred mouse strains
- Gene Cutler,
- Lisa A. Marshall,
- Ni Chin,
- Helene Baribault,
- and Paul D. Kassner
Genome Res. December 2007 17: 1743-1754; Published in Advance November 7, 2007, doi:10.1101/gr.6754607
...of quantitative real-time PCR . Nat. Methods 2 : 313 – 316 . ↵ Navarro, M. , de Rodriquez Fonseca, F. , Alvarez, E. , Chowen, J.A. , Zueco, J.A. , Gomez, R. , Eng, J. , Blazquez, E. ( 1996 ) Colocalization of glucagon-like peptide-1 (GLP-1) receptors, glucose transporter GLUT-2, and glucokinase mRNAs in rat...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
...of next-generation sequence assembly. Nat Methods 8: 61–65. Atanur SS, Diaz AG,Maratou K, Sarkis A, RotivalM,Game L, TschannenMR, Kaisaki PJ, Otto GW, Ma MC, et al. 2013. Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell 154: 691...
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LETTER: Genetic and Haplotype Diversity Among Wild-Derived Mouse Inbred Strains
- Folami Y. Ideraabdullah,
- Elena de la Casa-Esperón,
- Timothy A. Bell,
- David A. Detwiler,
- Terry Magnuson,
- Carmen Sapienza,
- and Fernando Pardo-Manuel de Villena
Genome Res. October 2004 14: 1880-1887; doi:10.1101/gr.2519704
...connecting the specific and subspecific divergence nodes (b in Fig. 2 ) depends on the correct identification of the ancestral allele, we tested whether our predictions are supported by the allele found at homologous positions in the rat. The predicted ancestral allele is supported by the rat sequence at 82...
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LETTER: Genetic variation in the zebrafish
- Victor Guryev,
- Marco J. Koudijs,
- Eugene Berezikov,
- Stephen L. Johnson,
- Ronald H.A. Plasterk,
- Fredericus J.M. van Eeden,
- and Edwin Cuppen
Genome Res. April 2006 16: 491-497; Published in Advance March 13, 2006, doi:10.1101/gr.4791006
...inbred strains differ from other commonly used vertebrate laboratory animals such as inbred mouse or rat strains. Finally, the analysis of genotype data contributes to better understanding of strain history and the degree of interstrain variation. The variety of methods used to generate inbred lines, e...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
...different inbred strains and provides a measurement of relatedness between these inbred strains. This tool creates a visual haplotype that can be used to identify conserved and nonconserved chromosomal regions between any of the 48 rat strains characterized as part of the Allele Characterization Project...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
...and within commonly used inbred rat strains. Genome Res. (this issue). ↵ Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., et al. 2002 . The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12 : 1611 –1618...
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RESOURCE: Applications of a Rat Multiple Tissue Gene Expression Data Set
- John R. Walker,
- Andrew I. Su,
- David W. Self,
- John B. Hogenesch,
- Hilmar Lapp,
- Rainer Maier,
- Daniel Hoyer,
- and Graeme Bilbe
Genome Res. April 2004 14: 742-749; doi:10.1101/gr.2161804
...expression across multiple tissues ( Mootha et al. 2003 ). Here, we examine normal physiological expression levels of ∼7000 characterized rat genes and 1000 EST clusters in 11 peripheral and 15 brain regions in three common out-bred rat strains. We describe various applications of this data set including (1...
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REVIEW: The influence of genetic variation on gene expression
- Rohan B.H. Williams,
- Eva K.F. Chan,
- Mark J. Cowley,
- and Peter F.R. Little
Genome Res. December 2007 17: 1707-1716; doi:10.1101/gr.6981507
...compared with trans -acting eQTLs have a stronger and more detectable influence on gene expression. Petretto et al. (2006) analyzed four tissues in the rat and showed that trans -eQTLs generally have smaller effect size and higher false discovery rates than cis -eQTLs. Overall, a general conclusion from...

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