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Data released on April 11, 2014

Genomic data of the Chinese tree shrew (Tupaia chinensis).

Cao, C; Chen, C; Chen, Y; Fan, D; Fan, Y; He, J; Hou, H; Hu, L; Hu, X; Huang, Z; Jiang, X; Lai, R; Lang, Y; Liang, B; Liao, S; Ma, Y; Mu, D; Niu, Y; Sun, X; Xia, J; Xiao, J; Xiong, Z; Xu, L; Yang, L; Zhang, Y; Zhao, W; Zhao, X; Zheng, Y; Zhou, J; Zhang, G; Zhu, Y (2014): Genomic data of the Chinese tree shrew (Tupaia chinensis). GigaScience Database. http://dx.doi.org/10.5524/100072 RIS BibTeX Text

Chinese tree shrews (Tupaia belangeri chinensis) possess many features valuable in animals used as experimental models in biomedical research. Currently, there are numerous attempts to employ tree shrews as models for a variety of human disorders: depression, myopia, hepatitis B and C virus infections, and hepatocellular carcinoma, to name a few. Here we present a publicly available annotated genome sequence for the Chinese tree shrew. Phylogenomic analysis of the tree shrew and other mammalians highly support its close affinity to primates.

DNA form the tree shrew was collected in Yunnan, China. We sequenced the 3.2 Gb genome to a depth of approximately 79.2x with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and 40kb).
The assembled scaffolds of high quality sequences total 253.5 Gb, with the contig and scaffold N50 values of 22 kb and 3.65 Mb respectively. We identified 22,063 protein-coding genes.
Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).

Contact Submitter

Related manuscripts:

doi:10.1038/ncomms2416 (PubMed: 23385571)

Accessions (data included in GigaDB):

BioProject: PRJNA169406

Projects:


Genomic

http://gigadb.org/images/data/cropped/100072.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS347509246437Tupaia chinensisChinese tree shrew Sex:male
Geographic location (country and/or sea,region):Ch...
Geographic location (latitude and longitude):not r...
...
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Displaying 1-1 of 1 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 
ReadmeTEXT0.38 KB2014-04-11
SRS347509AnnotationGFF40.91 MB2014-04-11
SRS347509Coding sequenceFASTA26.41 MB2014-04-11
SRS347509Sequence assemblyFASTA2.67 GB2014-04-11
SRS347509Protein sequenceFASTA9.81 MB2014-04-11
Displaying 1-5 of 5 File(s).

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