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Data released on May 29, 2013

Whole-Genome Sequences of DA and F344 Rats with Different Susceptibilities to Arthritis, Autoimmunity, Inflammation and Cancer

Brenner, M; Gulko, P, S; Guo, X (2013): Whole-Genome Sequences of DA and F344 Rats with Different Susceptibilities to Arthritis, Autoimmunity, Inflammation and Cancer GigaScience Database. http://dx.doi.org/10.5524/100042 RIS BibTeX Text

DA and F344 are two inbred rat strains with numerous dichotomous phenotypes, including susceptibility to autoimmune disease models and inflammatory responses. While these strains have been extensively studied, little information is available about the DA and F344 genomes, as only the BN and SHR strains have been sequenced to date. Here we report the sequencing of the DA and F344 genomes using next-generation Illumina paired-end read technology, and the first de novo assembly of a rat genome. DA and F344 were sequenced with an average depth of 32- fold, covered 98.9% of the BN reference genome, and included 97.97% of known rat ESTs. New sequences could be assigned to 59 million positions with previously unknown data in the BN reference genome. Differences between DA, F344 and BN included 19 million positions in novel scaffolds, 4.09 million SNPs (including 1.37 million new SNPs), 458,224 short insertions and deletions, and 58,174 structural variants. Genetic differences between DA, F344, and BN, including high-impact SNPs and short insertions and deletions affecting over 2,500 genes, are likely to account for most of the phenotypic variation between these strains. The new DA and F344 genome sequencing data should facilitate gene discovery efforts in rat models of human disease.

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Related manuscripts:

doi:10.1534/genetics.113.153049 (PubMed: 23695301)

Accessions (data not in GigaDB):

SRA: SRP008537

Genomic

http://gigadb.org/images/data/cropped/100042_Brownrat.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS26571710116Brown RatNorway ratRattus norvegicus Strain:DA
SRS26571810116Brown RatNorway ratRattus norvegicus Strain:F344
Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
SRS265718Genome sequenceFASTQ5.28 GB2013-05-29
SRS265718Genome sequenceFASTQ5.06 GB2013-05-29
SRS265717Genome sequenceFASTQ6.7 GB2013-05-29
SRS265717Genome sequenceFASTQ6.44 GB2013-05-29
SRS265717Genome sequenceFASTQ6 GB2013-05-29
SRS265717Genome sequenceFASTQ5.79 GB2013-05-29
SRS265718Genome sequenceFASTQ5.72 GB2013-05-29
SRS265718Genome sequenceFASTQ5.51 GB2013-05-29
SRS265718Genome sequenceFASTQ3.84 GB2013-05-29
SRS265718Genome sequenceFASTQ3.86 GB2013-05-29
Displaying 1-10 of 53 File(s).

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