MoG+: a database of genomic variations across three mouse subspecies for biomedical research
Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus -derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M . m . domesticus -derived PGN2/Ms and B...
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creator | Takada, Toyoyuki Fukuta, Kentaro Usuda, Daiki Kushida, Tatsuya Kondo, Shinji Kawamoto, Shoko Yoshiki, Atsushi Obata, Yuichi Fujiyama, Asao Toyoda, Atsushi Noguchi, Hideki Shiroishi, Toshihiko Masuya, Hiroshi |
description | Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains:
Mus musculus musculus
-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms;
M
.
m
.
domesticus
-derived PGN2/Ms and BFM/Ms;
M
.
m
.
castaneus
-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between
M
.
m
.
musculus
and
M
.
m
.
castaneus
. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains. |
doi_str_mv | 10.1007/s00335-021-09933-w |
format | Article |
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Mus musculus musculus
-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms;
M
.
m
.
domesticus
-derived PGN2/Ms and BFM/Ms;
M
.
m
.
castaneus
-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between
M
.
m
.
musculus
and
M
.
m
.
castaneus
. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.</description><identifier>ISSN: 0938-8990</identifier><identifier>ISSN: 1432-1777</identifier><identifier>EISSN: 1432-1777</identifier><identifier>DOI: 10.1007/s00335-021-09933-w</identifier><identifier>PMID: 34782917</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Amino acids ; Animal Genetics and Genomics ; Animals ; Biomedical and Life Sciences ; Biomedical Research ; Body size ; Cell Biology ; Databases, Genetic ; Genetic distance ; Genome ; Genomes ; Genomic analysis ; Genomics ; Genotypes ; Human Genetics ; Inbreeding ; Life Sciences ; Medical research ; Mice ; Mice, Inbred Strains - genetics ; Nucleotides ; Oligodendrocyte-myelin glycoprotein ; Phenotypes ; Phenotypic variations ; Rodents ; Single-nucleotide polymorphism ; Strains (organisms)</subject><ispartof>Mammalian genome, 2022-03, Vol.33 (1), p.31-43</ispartof><rights>The Author(s) 2021</rights><rights>2021. The Author(s).</rights><rights>The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c455w-e8a10143ff1b56475e16262e61588e8d8ff1b0ec5256b16a6767c058ab9c4933</citedby><cites>FETCH-LOGICAL-c455w-e8a10143ff1b56475e16262e61588e8d8ff1b0ec5256b16a6767c058ab9c4933</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00335-021-09933-w$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00335-021-09933-w$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34782917$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Takada, Toyoyuki</creatorcontrib><creatorcontrib>Fukuta, Kentaro</creatorcontrib><creatorcontrib>Usuda, Daiki</creatorcontrib><creatorcontrib>Kushida, Tatsuya</creatorcontrib><creatorcontrib>Kondo, Shinji</creatorcontrib><creatorcontrib>Kawamoto, Shoko</creatorcontrib><creatorcontrib>Yoshiki, Atsushi</creatorcontrib><creatorcontrib>Obata, Yuichi</creatorcontrib><creatorcontrib>Fujiyama, Asao</creatorcontrib><creatorcontrib>Toyoda, Atsushi</creatorcontrib><creatorcontrib>Noguchi, Hideki</creatorcontrib><creatorcontrib>Shiroishi, Toshihiko</creatorcontrib><creatorcontrib>Masuya, Hiroshi</creatorcontrib><title>MoG+: a database of genomic variations across three mouse subspecies for biomedical research</title><title>Mammalian genome</title><addtitle>Mamm Genome</addtitle><addtitle>Mamm Genome</addtitle><description>Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains:
Mus musculus musculus
-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms;
M
.
m
.
domesticus
-derived PGN2/Ms and BFM/Ms;
M
.
m
.
castaneus
-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between
M
.
m
.
musculus
and
M
.
m
.
castaneus
. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.</description><subject>Amino acids</subject><subject>Animal Genetics and Genomics</subject><subject>Animals</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedical Research</subject><subject>Body size</subject><subject>Cell Biology</subject><subject>Databases, Genetic</subject><subject>Genetic distance</subject><subject>Genome</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Human Genetics</subject><subject>Inbreeding</subject><subject>Life Sciences</subject><subject>Medical research</subject><subject>Mice</subject><subject>Mice, Inbred Strains - genetics</subject><subject>Nucleotides</subject><subject>Oligodendrocyte-myelin glycoprotein</subject><subject>Phenotypes</subject><subject>Phenotypic variations</subject><subject>Rodents</subject><subject>Single-nucleotide polymorphism</subject><subject>Strains (organisms)</subject><issn>0938-8990</issn><issn>1432-1777</issn><issn>1432-1777</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kUtvFDEQhC0EIkvgD3BAlrggRQNte_ziEAlFISAFcckRyfJ4e3YdzYwXeyYr_j1ONoTHgZMP9XW5q4uQlwzeMgD9rgAIIRvgrAFrhWj2j8iKtYI3TGv9mKzACtMYa-GIPCvlGoBpxfRTciRabbhlekW-fUkXJ--pp2s_-84XpKmnG5zSGAO98Tn6OaapUB9yKoXO24xIx7RUsCxd2WGIWGifMu1iGnEdgx9oxoI-h-1z8qT3Q8EX9-8xufp4fnX2qbn8evH57MNlE1op9w0az6Du3fesk6rVEpniiqNi0hg0a3MrAAbJpeqY8korHUAa39nQ1tzH5PRgu1u6ukLAac5-cLscR59_uOSj-1uZ4tZt0o0zlolWmWrw5t4gp-8LltmNsQQcBj9hjeq4tAYMtKqt6Ot_0Ou05Kmmc1wJbVjNYSvFD9Td1TL2D8swcLfduUN3rnbn7rpz-zr06s8YDyO_yqqAOAClStMG8--__2P7EwZYpak</recordid><startdate>20220301</startdate><enddate>20220301</enddate><creator>Takada, Toyoyuki</creator><creator>Fukuta, Kentaro</creator><creator>Usuda, Daiki</creator><creator>Kushida, Tatsuya</creator><creator>Kondo, Shinji</creator><creator>Kawamoto, Shoko</creator><creator>Yoshiki, Atsushi</creator><creator>Obata, Yuichi</creator><creator>Fujiyama, Asao</creator><creator>Toyoda, Atsushi</creator><creator>Noguchi, Hideki</creator><creator>Shiroishi, Toshihiko</creator><creator>Masuya, Hiroshi</creator><general>Springer US</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20220301</creationdate><title>MoG+: a database of genomic variations across three mouse subspecies for biomedical research</title><author>Takada, Toyoyuki ; Fukuta, Kentaro ; Usuda, Daiki ; Kushida, Tatsuya ; Kondo, Shinji ; Kawamoto, Shoko ; Yoshiki, Atsushi ; Obata, Yuichi ; Fujiyama, Asao ; Toyoda, Atsushi ; Noguchi, Hideki ; Shiroishi, Toshihiko ; Masuya, Hiroshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c455w-e8a10143ff1b56475e16262e61588e8d8ff1b0ec5256b16a6767c058ab9c4933</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amino acids</topic><topic>Animal Genetics and Genomics</topic><topic>Animals</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedical Research</topic><topic>Body size</topic><topic>Cell Biology</topic><topic>Databases, Genetic</topic><topic>Genetic distance</topic><topic>Genome</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Genomics</topic><topic>Genotypes</topic><topic>Human Genetics</topic><topic>Inbreeding</topic><topic>Life Sciences</topic><topic>Medical research</topic><topic>Mice</topic><topic>Mice, Inbred Strains - genetics</topic><topic>Nucleotides</topic><topic>Oligodendrocyte-myelin glycoprotein</topic><topic>Phenotypes</topic><topic>Phenotypic variations</topic><topic>Rodents</topic><topic>Single-nucleotide polymorphism</topic><topic>Strains (organisms)</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Takada, Toyoyuki</creatorcontrib><creatorcontrib>Fukuta, Kentaro</creatorcontrib><creatorcontrib>Usuda, Daiki</creatorcontrib><creatorcontrib>Kushida, Tatsuya</creatorcontrib><creatorcontrib>Kondo, Shinji</creatorcontrib><creatorcontrib>Kawamoto, Shoko</creatorcontrib><creatorcontrib>Yoshiki, Atsushi</creatorcontrib><creatorcontrib>Obata, Yuichi</creatorcontrib><creatorcontrib>Fujiyama, Asao</creatorcontrib><creatorcontrib>Toyoda, Atsushi</creatorcontrib><creatorcontrib>Noguchi, Hideki</creatorcontrib><creatorcontrib>Shiroishi, Toshihiko</creatorcontrib><creatorcontrib>Masuya, Hiroshi</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Mammalian genome</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Takada, Toyoyuki</au><au>Fukuta, Kentaro</au><au>Usuda, Daiki</au><au>Kushida, Tatsuya</au><au>Kondo, Shinji</au><au>Kawamoto, Shoko</au><au>Yoshiki, Atsushi</au><au>Obata, Yuichi</au><au>Fujiyama, Asao</au><au>Toyoda, Atsushi</au><au>Noguchi, Hideki</au><au>Shiroishi, Toshihiko</au><au>Masuya, Hiroshi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MoG+: a database of genomic variations across three mouse subspecies for biomedical research</atitle><jtitle>Mammalian genome</jtitle><stitle>Mamm Genome</stitle><addtitle>Mamm Genome</addtitle><date>2022-03-01</date><risdate>2022</risdate><volume>33</volume><issue>1</issue><spage>31</spage><epage>43</epage><pages>31-43</pages><issn>0938-8990</issn><issn>1432-1777</issn><eissn>1432-1777</eissn><abstract>Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains:
Mus musculus musculus
-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms;
M
.
m
.
domesticus
-derived PGN2/Ms and BFM/Ms;
M
.
m
.
castaneus
-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between
M
.
m
.
musculus
and
M
.
m
.
castaneus
. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>34782917</pmid><doi>10.1007/s00335-021-09933-w</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; SpringerNature Journals |
subjects | Amino acids Animal Genetics and Genomics Animals Biomedical and Life Sciences Biomedical Research Body size Cell Biology Databases, Genetic Genetic distance Genome Genomes Genomic analysis Genomics Genotypes Human Genetics Inbreeding Life Sciences Medical research Mice Mice, Inbred Strains - genetics Nucleotides Oligodendrocyte-myelin glycoprotein Phenotypes Phenotypic variations Rodents Single-nucleotide polymorphism Strains (organisms) |
title | MoG+: a database of genomic variations across three mouse subspecies for biomedical research |
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