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Data released on April 21, 2015

Supporting data and materials for "De Novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences".

Madison, J, D; Maudhoo, M, D; Norgren Jr, R, B (2015): Supporting data and materials for "De Novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences". GigaScience Database. http://dx.doi.org/10.5524/100137 RIS BibTeX Text

Common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the species most closely related to humans. For this reason, it is especially important to have complete and accurate chimpanzee nucleotide and protein sequences to understand how humans evolved their unique capabilities. We provide transcriptome data from four untransformed cell types derived from the reference Pan troglodytes “Clint”, to better annotate the chimpanzee genome and provide empirical validation for proposed gene models of this important species. RNA was extracted from primary cells cultured from four tissues: skin, adipose stroma, vascular smooth muscle, and skeletal muscle. These four RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the Sequence Read Archive (SRA). Transcripts were assembled, annotated and deposited in the INSDC Transcriptome Shotgun Assembly (TSA) database. We have provided a high quality annotation of 44,275 transcripts with full-length coding sequence (CDS). This set represented a total of 10,110 unique genes, thus providing empirical support for their existence. This dataset can be used to improve annoannotation of the Pan troglodytes genome.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0061-x

Accessions (data included in GigaDB):

BioProject: PRJNA173089
ENA: GABD01000000
ENA: GABC01000000
ENA: GABF01000000
ENA: GABE01000000

Keywords:

Pan troglodytes chimpanzee transcriptome mRNA-seq assembly 

Transcriptomic

http://gigadb.org/images/data/cropped/100137.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRX1792649598 chimpanzeePan troglodytes Cell type:Stem cells
Tissue type:Adipose stroma
Alternative accession-INSDC:GABC01000001–GABC010...
...
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SRX1792669598 chimpanzeePan troglodytes Cell type:Endothelial cells
Tissue type:Vascular smooth muscle
Alternative accession-INSDC:GABF01000001–GABF010...
...
+
SRX1792679598 chimpanzeePan troglodytes Cell type:Fibroblasts
Tissue type:Skin
Alternative accession-INSDC:GABD01000001–GABD010...
...
+
SRX1792719598 chimpanzeePan troglodytes Cell type:Myoblasts
Tissue type:Skeletal muscle
Alternative accession-INSDC:GABE01000001–GABE010...
...
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Displaying 1-4 of 4 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 
ISA-Tabzip4.71 KB2015-05-28
ReadmeTEXT1.62 KB2015-04-09
Displaying 1-2 of 2 File(s).

History:

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