Rat Genome Sequencing

The National Human Genome Research Institute (NHGRI) and the National Heart, Lung and Blood Institute (NHLBI) have supported a rat genome sequencing project to produce 7X draft coverage of the rat genome in a mixture of whole genome shotgun and Bacterial Artificial Chromosome (BAC)-based sequence. The resulting genome sequence was assembled in March, 2004 (to see NIH press release, please click here).

The Rat Genome Sequencing Network is led by the Baylor College of Medicine Genome Sequencing Center and is a collaboration with Celera Genomics, Genome Therapeutics, The Institute for Genome Research and The University of British Columbia.

Genome Sequencing Whitepaper Proposals:

 

• Rattus norvegicus
  Rat SNPs / SNP Discovery
  (Submitted Oct. 2004)
   
• Rattus norvegicus
  Genome Refinement
  (Submitted Sept. 2005)

Project Links:

• Baylor College of Medicine Genome Sequencing Center [hgsc.bcm.tmc.edu]
• The Gene Index Project [compbio.dfci.harvard.edu]

Supporting Institutions:

• NHLBI [nhlbi.nih.gov]

Collaborating Organizations:

• Celera Genomics [celera.com]
• Canada's Michael Smith Genome Sciences Centre [bcgsc.bc.ca]

The Trans-NIH Rat Program [nih.gov] is an excellent source of additional information of a wide range of genomic and genetic resources related to the laboratory rat.

Additional Resources

Sequence and Assembly

• Individual sequence reads:
  • NCBI Trace Archives
• Sequence Assemblies:
  • Ensembl
  • NCBI
  • UCSC

Model Organism Database

• Rat Genome Database [rgd.mcw.edu] at the Medical College of Wisconsin

Mapping

• Genome Sciences Centre [bcgsc.ca] at the British Columbia Cancer Agency

BAC End Sequencing

• Dana Farber Cancer Institute (DCFI) [compbio.dfci.harvard.edu]*
  * TGI databases have moved at DFCI and are no longer available at TIGR/JCVI.

ESTs

• dbEST [ncbi.nlm.nih.gov] - Database of ESTs at NCBI

cDNAs

• Mammalian Gene Collection [mgc.nci.nih.gov]

SNPs

• dbSNP [ncbi.nlm.nih.gov] - Database of Single Nucleotide Polymorphisms at NCBI

BAC Libraries

• Childrens Hospital Oakland Research Institute (CHORI) - Rat BAC libraries
  • RPCI-31: Brown Norway Rat (F) PAC Library [bacpac.chori.org]
  • RPCI-32: Brown Norway Rat (M) BAC Library [bacpac.chori.org]
  • CHORI-230: Brown Norway Rat BN/SsNHsd/MCW (F) BAC Library [bacpac.chori.org]
     
• Rat (Multiple Strains) BAC Library Proposal