Mammalian genome : official journal of the International Mammalian Genome Society最新文献_第3页

Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes. 多基因组查看器(Multiple genome viewer, MGV):一种用于多个注释基因组可视化和比较的新工具。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2021-08-27 DOI: 10.1007/s00335-021-09904-1

Joel E Richardson, Richard M Baldarelli, Carol J Bult

{"title":"Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes.","authors":"Joel E Richardson, Richard M Baldarelli, Carol J Bult","doi":"10.1007/s00335-021-09904-1","DOIUrl":"https://doi.org/10.1007/s00335-021-09904-1","url":null,"abstract":"The assembled and annotated genomes for 16 inbred mouse strains (Lilue et al., Nat Genet 50:1574-1583, 2018) and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) (Thybert et al., Genome Res 28:448-459, 2018) are valuable resources for mouse genetics and comparative genomics. We developed the multiple genome viewer (MGV; http://www.informatics.jax.org/mgv ) to support visualization, exploration, and comparison of genome annotations within and across these genomes. MGV displays chromosomal regions of user-selected genomes as horizontal tracks. Equivalent features across the genome tracks are highlighted using vertical 'swim lane' connectors. Navigation across the genomes is synchronized as a researcher uses the scroll and zoom functions. Researchers can generate custom sets of genes and other genome features to be displayed in MGV by entering genome coordinates, function, phenotype, disease, and/or pathway terms. MGV was developed to be genome agnostic and can be used to display homologous features across genomes of different organisms.","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"44-54"},"PeriodicalIF":2.5,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-021-09904-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39357899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

The mouse resource at National Resource Center for Mutant Mice. 国家突变小鼠资源中心的小鼠资源。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2022-02-09 DOI: 10.1007/s00335-021-09940-x

Cunxiang Ju, Juan Liang, Mingkun Zhang, Jinlong Zhao, Ling'en Li, Shuai Chen, Jing Zhao, Xiang Gao

引用次数: 1

Importing genetically altered animals: ensuring quality. 进口转基因动物：确保质量。

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2021-09-18 DOI: 10.1007/s00335-021-09908-x

M-C Birling, M D Fray, P Kasparek, J Kopkanova, M Massimi, R Matteoni, L Montoliu, L M J Nutter, M Raspa, J Rozman, E J Ryder, F Scavizzi, V Voikar, S Wells, G Pavlovic, L Teboul

引用次数: 0

Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource. 小鼠重组酶等位基因和转基因的注释表达和活性数据:CrePortal资源。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2021-09-04 DOI: 10.1007/s00335-021-09909-w

Michelle N Perry, Constance M Smith, Hiroaki Onda, Martin Ringwald, Stephen A Murray, Cynthia L Smith

{"title":"Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource.","authors":"Michelle N Perry, Constance M Smith, Hiroaki Onda, Martin Ringwald, Stephen A Murray, Cynthia L Smith","doi":"10.1007/s00335-021-09909-w","DOIUrl":"https://doi.org/10.1007/s00335-021-09909-w","url":null,"abstract":"Recombinase alleles and transgenes can be used to facilitate spatio-temporal specificity of gene disruption or transgene expression. However, the versatility of this in vivo recombination system relies on having detailed and accurate characterization of recombinase expression and activity to enable selection of the appropriate allele or transgene. The CrePortal ( http://www.informatics.jax.org/home/recombinase ) leverages the informatics infrastructure of Mouse Genome Informatics to integrate data from the scientific literature, direct data submissions from the scientific community at-large, and from major projects developing new recombinase lines and characterizing recombinase expression and specificity patterns. Searching the CrePortal by recombinase activity or specific recombinase gene driver provides users with a recombinase alleles and transgenes activity tissue summary and matrix comparison of gene expression and recombinase activity with links to generation details, a recombinase activity grid, and associated phenotype annotations. Future improvements will add cell type-based activity annotations. The CrePortal provides a comprehensive presentation of recombinase allele and transgene data to assist researchers in selection of the recombinase allele or transgene based on where and when recombination is desired.","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"55-65"},"PeriodicalIF":2.5,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8913597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39385294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Genomic resources for rhesus macaques (Macaca mulatta). 恒河猴基因组资源。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2022-01-09 DOI: 10.1007/s00335-021-09922-z

Jeffrey Rogers

{"title":"Genomic resources for rhesus macaques (Macaca mulatta).","authors":"Jeffrey Rogers","doi":"10.1007/s00335-021-09922-z","DOIUrl":"https://doi.org/10.1007/s00335-021-09922-z","url":null,"abstract":"Rhesus macaques (Macaca mulatta) are among the most extensively studied of nonhuman primates. This species has been the subject of many investigations concerning basic primate biology and behavior, including studies of social organization, developmental psychology, physiology, endocrinology, and neurodevelopment. Rhesus macaques are also critically important as a nonhuman primate model of human health and disease, including use in studies of infectious diseases, metabolic diseases, aging, and drug or alcohol abuse. Current research addressing fundamental biological and/or applied biomedical questions benefits from various genetic and genomic analyses. As a result, the genome of rhesus macaques has been the subject of more study than most nonhuman primates. This paper briefly discusses a number of information resources that can provide interested researchers with access to genetic and genomic data describing the content of the rhesus macaque genome, available information regarding genetic variation within the species, results from studies of gene expression, and other aspects of genomic analysis. Specific online databases are discussed, including the US National Center for Biotechnology Information, the University of California Santa Cruz genome browser, Ensembl genome browser, the Macaque Genotype and Phenotype database (mGAP), Rhesusbase, and others.","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"91-99"},"PeriodicalIF":2.5,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8742695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39797303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Introduction to Mammalian Genome Special Issue: Mammalian Genetic Resources. 哺乳动物基因组导论特刊：哺乳动物遗传资源。

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 DOI: 10.1007/s00335-022-09942-3

Steve D M Brown, Joseph H Nadeau, Sara Wells, Ann-Marie Mallon, Lydia Teboul, Christopher K Tuggle, Lawrence B Schook

引用次数: 0

Nonhuman primates' tissue banks: resources for all model organism research. 非人类灵长类动物的组织库：所有模式生物研究的资源。

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2021-10-26 DOI: 10.1007/s00335-021-09925-w

Claire Witham, Sara Wells

引用次数: 0

Mouse genomic and cellular annotations. 小鼠基因组和细胞注释。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2022-02-05 DOI: 10.1007/s00335-021-09936-7

Helen Long, Richard Reeves, Michelle M Simon

{"title":"Mouse genomic and cellular annotations.","authors":"Helen Long, Richard Reeves, Michelle M Simon","doi":"10.1007/s00335-021-09936-7","DOIUrl":"https://doi.org/10.1007/s00335-021-09936-7","url":null,"abstract":"Mice have emerged as one of the most popular and valuable model organisms in the research of human biology. This is due to their genetic and physiological similarity to humans, short generation times, availability of genetically homologous inbred strains, and relatively easy laboratory maintenance. Therefore, following the release of the initial human reference genome, the generation of the mouse reference genome was prioritised and represented an important scientific resource for the mouse genetics community. In 2002, the Mouse Genome Sequencing Consortium published an initial draft of the mouse reference genome which contained ~ 96% of the euchromatic genome of female C57BL/6 J mice. Almost two decades on from the publication of the initial draft, sequencing efforts have continued to increase the completeness and accuracy of the C57BL/6 J reference genome alongside advances in genome annotation. Additionally new sequencing technologies have provided a wealth of data that has added to the repertoire of annotations associated with traditional genomic annotations. Including but not limited to advances in regulatory elements, the 3D genome and individual cellular states. In this review we focus on the reference genome C57BL/6 J and summarise the different aspects of genomic and cellular annotations, as well as their relevance to mouse genetic research. We denote a genomic annotation as a functional unit of the genome. Cellular annotations are annotations of cell type or state, defined by the transcriptomic expression profile of a cell. Due to the wide-ranging number and diversity of annotations describing the mouse genome, we focus on gene, repeat and regulatory element annotation as well as two relatively new technologies; 3D genome architecture and single-cell sequencing outlining their utility in genetic research and their current challenges.","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"19-30"},"PeriodicalIF":2.5,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8913471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39892490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Coding variants in mouse and rat model organisms: mousepost and ratpost. 小鼠和大鼠模式生物的编码变异:mousepost和ratpost。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2021-07-27 DOI: 10.1007/s00335-021-09898-w

Steven Timmermans, Claude Libert

{"title":"Coding variants in mouse and rat model organisms: mousepost and ratpost.","authors":"Steven Timmermans, Claude Libert","doi":"10.1007/s00335-021-09898-w","DOIUrl":"https://doi.org/10.1007/s00335-021-09898-w","url":null,"abstract":"Mice and rats are the most commonly used vertebrate model organisms in biomedical research. The availability of a reference genome in both animals combined with the deep sequencing of several doze of popular inbred lines also provides rich sequence variation data in these species. In some cases, such sequence variants can be linked directly to a distinctive phenotype. In previous work, we created the mouse and rat online searchable databases (\"Mousepost\" and \"Ratpost\") where small variant information for protein coding transcripts in mouse and rat inbred strains can be easily retrieved at the amino acid level. These tools are directly useful in forward genetics strategies or as a repository of existing sequence variations. Here, we perform a comparison between the \"Mousepost\" and \"Ratpost\" databases and we couple these two tools to a database of human sequence variants ClinVar. We investigated the level of redundancy and complementarity of known variants in protein coding transcripts and found that the large majority of variants is species-specific. However, a small set of positions is conserved in an inbred line between both species. We conclude that both databases are highly complementary, but this may change with further sequencing efforts in both species.","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"81-87"},"PeriodicalIF":2.5,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-021-09898-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39227147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Fast and efficient generation of a full-length balancer chromosome by a single Cre/loxP recombination event. 通过单个Cre/loxP重组事件快速高效地生成全长平衡染色体。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2022-03-01 Epub Date: 2021-08-12 DOI: 10.1007/s00335-021-09897-x

Cunxiang Ju, Mingkun Zhang, Min Guan, Song Li, Yuxi Zhang, Jing Zhao, Xiang Gao

{"title":"Fast and efficient generation of a full-length balancer chromosome by a single Cre/loxP recombination event.","authors":"Cunxiang Ju, Mingkun Zhang, Min Guan, Song Li, Yuxi Zhang, Jing Zhao, Xiang Gao","doi":"10.1007/s00335-021-09897-x","DOIUrl":"https://doi.org/10.1007/s00335-021-09897-x","url":null,"abstract":"Balancer chromosomes, primarily discovered and used in Drosophila melanogaster, are valuable tools to maintain lethal mutations in a particular genomic segment. Full-length balancer chromosomes would be particularly useful because of the capacity to maintain whole genomic traits. However, murine full-length balancer chromosomes generated via a single Cre/loxP recombination are still not demonstrated. In this study, we developed a novel mouse strain with full-length inverted chromosome 17 (Ch17Inv balancer) via a single Cre/loxP recombination event in mES cells. The Ch17Inv balancer mice are viable and phenotypically normal. When bred with other strains, the haplotype of chromosome 17 can be stably maintained as determined by the high throughput SNPs assay. Interestingly, we found that the recombination events were efficiently reduced within the inverted region but not eliminated. The method established in this study can be applied to generate other full-length balancer chromosomes. Moreover, the Ch17Inv balancer strain would be a valuable resource to maintain the entire chromosome 17 from different donor strains.","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"169-180"},"PeriodicalIF":2.5,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-021-09897-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39306380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1