Abstract
Resources for rat researchers are extensive, including strain repositories and databases all around the world. The Rat Genome Database (RGD) serves as the primary rat data repository, providing both manual and computationally collected data from other databases.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Worthey EA, Stoddard AJ, Jacob HJ (2010) Sequencing of the rat genome and databases. Methods Mol Biol 597:33–53. https://doi.org/10.1007/978-1-60327-389-3_3
Richter CP (1954) The effects of domestication and selection on the behavior of the Norway rat. J Natl Cancer Inst 15(3):727–738
Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L et al (2013) Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell 154(3):691–703. https://doi.org/10.1016/j.cell.2013.06.040
Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW et al (2013) Combined sequence-based and genetic map** analysis of complex traits in outbred rats. Nat Genet 45(7):767–775. https://doi.org/10.1038/ng.2644
Li D, Qiu Z, Shao Y, Chen Y, Guan Y, Liu M et al (2013) Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat Biotechnol 31(8):681–683. https://doi.org/10.1038/nbt.2661
Geurts AM, Moreno C (2010) Zinc-finger nucleases: new strategies to target the rat genome. Clin Sci (Lond) 119(8):303–311. https://doi.org/10.1042/cs20100201
Tong C, Huang G, Ashton C, Wu H, Yan H, Ying QL (2012) Rapid and cost-effective gene targeting in rat embryonic stem cells by TALENs. J Genet Genomics 39(6):275–280. https://doi.org/10.1016/j.jgg.2012.04.004
Carlson DF, Geurts AM, Garbe JR, Park CW, Rangel-Filho A, O'Grady SM et al (2011) Efficient mammalian germline transgenesis by cis-enhanced Slee** Beauty transposition. Transgenic Res 20(1):29–45. https://doi.org/10.1007/s11248-010-9386-5
Menoret S, Fontaniere S, Jantz D, Tesson L, Thinard R, Remy S et al (2013) Generation of Rag1-knockout immunodeficient rats and mice using engineered meganucleases. FASEB J 27(2):703–711. https://doi.org/10.1096/fj.12-219907
Serikawa T, Mashimo T, Takizawa A, Okajima R, Maedomari N, Kumafuji K et al (2009) National BioResource Project-Rat and related activities. Exp Anim 58(4):333–341
Mashimo T, Voigt B, Kuramoto T, Serikawa T (2005) Rat Phenome Project: the untapped potential of existing rat strains. J Appl Physiol 98(1):371–379. https://doi.org/10.1152/japplphysiol.01006.2004
Laulederkind SJ, Liu W, Smith JR, Hayman GT, Wang SJ, Nigam R et al (2013) PhenoMiner: quantitative phenotype curation at the rat genome database. Database 2013:bat015. https://doi.org/10.1093/database/bat015
Mashimo T, Voigt B, Tsurumi T, Naoi K, Nakanishi S, Yamasaki K et al (2006) A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains. BMC Genet 7:19. https://doi.org/10.1186/1471-2156-7-19
Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y et al (2008) SNP and haplotype map** for genetic analysis in the rat. Nat Genet 40(5):560–566. https://doi.org/10.1038/ng.124
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S et al (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982):493–521. https://doi.org/10.1038/nature02426
Hermsen R, de Ligt J, Spee W, Blokzijl F, Schafer S, Adami E et al (2015) Genomic landscape of rat strain and substrain variation. BMC Genomics 16:357. https://doi.org/10.1186/s12864-015-1594-1
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29. https://doi.org/10.1038/75556
Smith CL, Goldsmith CA, Eppig JT (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6(1):R7. https://doi.org/10.1186/gb-2004-6-1-r7
Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J et al (2014) The pathway ontology – updates and applications. J Biomed Semantics 5(1):7. https://doi.org/10.1186/2041-1480-5-7
Laulederkind SJ, Tutaj M, Shimoyama M, Hayman GT, Lowry TF, Nigam R et al (2012) Ontology searching and browsing at the Rat Genome Database. Database 2012:bas016. https://doi.org/10.1093/database/bas016
Nigam R, Munzenmaier DH, Worthey EA, Dwinell MR, Shimoyama M, Jacob HJ (2013) Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD. J Biomed Semantics 4(1):36. https://doi.org/10.1186/2041-1480-4-36
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F et al (2014) The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42(Database issue):D358–D363. https://doi.org/10.1093/nar/gkt1115
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S et al (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods 9(4):345–350. https://doi.org/10.1038/nmeth.1931
Skinner ME, Holmes IH (2010) Setting up the JBrowse genome browser. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis, et al. Chapter 9:Unit 9.13. https://doi.org/10.1002/0471250953.bi0913s32
Westesson O, Skinner M, Holmes I (2013) Visualizing next-generation sequencing data with JBrowse. Brief Bioinform 14(2):172–177. https://doi.org/10.1093/bib/bbr078
Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK et al (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res 45(D1):D369–d379. https://doi.org/10.1093/nar/gkw1102
Dwinell MR (2010) Online tools for understanding rat physiology. Brief Bioinform 11(4):431–439. https://doi.org/10.1093/bib/bbp069
Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M et al (2012) Multiscale modeling and data integration in the virtual physiological rat project. Ann Biomed Eng 40(11):2365–2378. https://doi.org/10.1007/s10439-012-0611-7
Yu Y, Fuscoe JC, Zhao C, Guo C, Jia M, Qing T et al (2014) A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat Commun 5:3230. https://doi.org/10.1038/ncomms4230
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J et al (2017) Ensembl 2017. Nucleic Acids Res 45(D1):D635–d642. https://doi.org/10.1093/nar/gkw1104
Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE et al (2014) The Vertebrate Genome Annotation browser 10 years on. Nucleic Acids Res 42(Database issue):D771–D779. https://doi.org/10.1093/nar/gkt1241
Tanabe M, Kanehisa M (2012) Using the KEGG database resource. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis. et al. Chapter 1:Unit1.12. https://doi.org/10.1002/0471250953.bi0112s38
Bhave SV, Hornbaker C, Phang TL, Saba L, Lapadat R, Kechris K et al (2007) The PhenoGen informatics website: tools for analyses of complex traits. BMC Genet 8:59. https://doi.org/10.1186/1471-2156-8-59
Acknowledgements
RGD is supported by the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health [HL64541].
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Laulederkind, S.J.F. et al. (2019). Rat Genome Databases, Repositories, and Tools. In: Hayman, G., Smith, J., Dwinell, M., Shimoyama, M. (eds) Rat Genomics. Methods in Molecular Biology, vol 2018. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9581-3_3
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9581-3_3
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9580-6
Online ISBN: 978-1-4939-9581-3
eBook Packages: Springer Protocols