Rat Genome Databases, Repositories, and Tools

  • Protocol
  • First Online:
Rat Genomics

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. 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

    Article  CAS  PubMed  Google Scholar 

  2. Richter CP (1954) The effects of domestication and selection on the behavior of the Norway rat. J Natl Cancer Inst 15(3):727–738

    CAS  PubMed  Google Scholar 

  3. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. 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

    Article  CAS  PubMed  Google Scholar 

  5. 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

    Article  CAS  PubMed  Google Scholar 

  6. 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

    Article  CAS  Google Scholar 

  7. 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

    Article  CAS  PubMed  Google Scholar 

  8. 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

    Article  CAS  PubMed  Google Scholar 

  9. 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

    Article  CAS  PubMed  Google Scholar 

  10. 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

    Article  CAS  PubMed  Google Scholar 

  11. 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

    Article  PubMed  Google Scholar 

  12. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. 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

    Article  CAS  PubMed  Google Scholar 

  16. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. 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

    Article  PubMed  Google Scholar 

  19. 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

    Article  PubMed  PubMed Central  Google Scholar 

  20. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. 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

    Article  PubMed  PubMed Central  Google Scholar 

  22. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. 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

    Article  CAS  PubMed  Google Scholar 

  24. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. 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

  26. 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

    Article  CAS  PubMed  Google Scholar 

  27. 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

    Article  CAS  PubMed  Google Scholar 

  28. Dwinell MR (2010) Online tools for understanding rat physiology. Brief Bioinform 11(4):431–439. https://doi.org/10.1093/bib/bbp069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. 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

    Article  PubMed  PubMed Central  Google Scholar 

  30. 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

    Article  CAS  PubMed  Google Scholar 

  31. 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

    Article  CAS  PubMed  Google Scholar 

  32. 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

    Article  CAS  PubMed  Google Scholar 

  33. 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

  34. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

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

Authors

Corresponding author

Correspondence to Stanley J. F. Laulederkind .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

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

Publish with us

Policies and ethics

Navigation