ArticlebioRxiv : the preprint server for biology2023
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.
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Authors and funding
51 authors.
Tristan V de JongDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Yanchao PanDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
Pasi RastasInstitute of Biotechnology, University of Helsinki, Helsinki, Finland.
Daniel MunroDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Monika TutajDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
Huda AkilMichigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
Chris BennerDepartment of Medicine, University of California San Diego, San Diego, CA, USA.
Denghui ChenDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Apurva S ChitreDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
William ChowTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Vincenza ColonnaInstitute of Genetics and Biophysics, National Research Council, Naples, Italy.
Clifton L DalgardDepartment of Anatomy, Physiology & Genetics; The American Genome Center, Uniformed Services University of the Health Sciences, Washington DC, USA.
Wendy M DemosDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
Peter A DorisThe Brown Foundation Institute of Molecular Medicine, Center For Human Genetics, University of Texas Health Science Center, Houston, TX, USA.
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Aron M GeurtsDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
Hakan M GunturkunDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Victor GuryevGenome Structure and Ageing, University of Groningen, UMC Groningen, The Netherlands.
Thibaut HourlierEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK.
Kerstin HoweTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Jun HuangDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Ted KalbfleischGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA.
Panjun KimDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Ling LiDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Spencer MahaffeyDepartment of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK.
Pejman MohammadiCenter for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA.
Ayse Bilge OzelDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
Oksana PolesskayaDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Michal PravenecInstitute of Physiology, Czech Academy of Sciences, Prague, Czechia.
Pjotr PrinsDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Jonathan SebatDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Jennifer R SmithDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
Leah C Solberg WoodsDepartment of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
Boris TabakoffDepartment of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Alan TraceyTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Marcela Uliano-SilvaTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Flavia VillaniDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Hongyang WangDepartment of Animal Sciences, Washington State University, Pullman, WA, USA.
Burt M SharpDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Francesca TeleseDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Zhihua JiangDepartment of Animal Sciences, Washington State University, Pullman, WA, USA.
Laura SabaDepartment of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Xusheng WangDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Terence D MurphyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Abraham A PalmerDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Anne E KwitekDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
Melinda R DwinellDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
Robert W WilliamsDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Jun Z LiDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
Hao ChenDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Funding
RAT GENOME DATABASER01HL064541 · NHLBI · MEDICAL COLLEGE OF WISCONSIN · PI ANNE E. KWITEK · 1999 to 2026
$50.0MText mining in the CloudU24HG010859 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAROL J BULT, PAUL Warren STERNBERG · 2019 to 2026
$42.0MSequencing CoreP50DA037844 · NIDA · UNIVERSITY OF CHICAGO · PI PALMER, ABRAHAM A · 2014 to 2023
$27.4MThe Heritable Transcriptome and AlcoholismR24AA013162 · NIAAA · UNIVERSITY OF COLORADO DENVER · PI HOFFMAN, PAULA, SABA, LAURA MAREN · 2001 to 2021
$14.2MSequencing Coordination and Data Analysis CoreP01HL149620 · NHLBI · UNIVERSITY OF ARIZONA · PI LIANG, MINGYU · 2020 to 2024
$11.8MInvestigating the role of Bmp4 in glial subtype specification and temperamentU01DA043098 · NIDA · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI HUDA AKIL, Jun Li · 2017 to 2026
$6.9MHybrid Rat Diversity Program - Import of HXB/BXH panelR24OD024617 · OD · MEDICAL COLLEGE OF WISCONSIN · PI DWINELL, MELINDA R · 2018 to 2025
$6.8MSingle-cell resolution analysis of chromatin accessibility and gene expression changes in a model of drug addictionU01DA050239 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GRAHAM MCVICKER, Abraham A Palmer · 2020 to 2026
$4.4MTIM Project NIDA P30 CenterP30DA044223 · NIDA · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI SEN, SAUNAK · 2017 to 2021
$3.9MThe role of structural variants and tandem repeats in substance abuse-related behavioral traitsU01DA051234 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GYMREK, MELISSA, PALMER, ABRAHAM A · 2021 to 2025
$3.5MDecoding the grammar of transcriptional enhancers regulating different stages of opioid use disorderU01DA051972 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BENNER, CHRISTOPHER W, TELESE, FRANCESCA · 2020 to 2024
$3.4MSystem genetics of menthol and nicotine addictionU01DA047638 · NIDA · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI CHEN, HAO, WILLIAMS, ROBERT W. · 2019 to 2023
$3.1MNHGRI NIH HHS R01 HG011252NHGRI NIH HHS U24 HG010859NHLBI NIH HHS P01 HL149620NHLBI NIH HHS R01 HL064541NHLBI NIH HHS R01 HL089895NIAAA NIH HHS R24 AA013162NIDA NIH HHS P30 DA044223NIDA NIH HHS P50 DA037844NIDA NIH HHS R01 DA048017NIDA NIH HHS U01 DA043098NIDA NIH HHS U01 DA047638NIDA NIH HHS U01 DA050239NIDA NIH HHS U01 DA051234NIDA NIH HHS U01 DA051972NIDDK NIH HHS R21 DK089417NIGMS NIH HHS R01 GM140287NIH HHS R24 OD024617Wellcome Trust
Abstract
The seventh iteration of the reference genome assembly for
Indexed as
Genetic MapHeterogeneous StockHybrid Rat Diversity PanelInbred StrainsmRatBN7.2Phylogenetic TreeRatRecombinant InbredReference GenomeRnor_6.0
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.