Supporting data and materials for "De Novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences".
Dataset type: Transcriptomic
Data released on April 21, 2015
Maudhoo MD; Madison JD; Norgren Jr RB (2015): Supporting data and materials for "De Novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences". GigaScience Database. https://doi.org/10.5524/100137
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.
Additional details
Read the peer-reviewed publication(s):
- Maudhoo, M. D., Madison, J. D., & Norgren, R. B. (2015). De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0061-x
Accessions (data included in GigaDB):
BioProject: PRJNA173089
ENA: GABD01000000
ENA: GABC01000000
ENA: GABF01000000
ENA: GABE01000000
Click on a table column to sort the results.
Table Settings| Sample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
|---|---|---|---|---|---|
| SRX179267 | Chimpanzee | Pan troglodytes | Tissue:Skin Cell type:Fibroblasts Alternative accession-INSDC:GABD01000001–GA... ... |
9598 | chimpanzee |
| SRX179264 | Chimpanzee | Pan troglodytes | Description:untransformed stem cells from adipose ... Tissue:Adipose stroma Cell type:Stem cells ... |
9598 | chimpanzee |
| SRX179266 | Chimpanzee | Pan troglodytes | Cell type:Endothelial cells Description:untransformed endothelial cells from ... Tissue:Vascular smooth muscle ... |
9598 | chimpanzee |
| SRX179271 | Chimpanzee | Pan troglodytes | Description:untransformed myoblasts from skeletal ... Cell type:Myoblasts Tissue:Skeletal muscle ... |
9598 | chimpanzee |
Click on a table column to sort the results.
Table Settings| File Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
|---|---|---|---|---|---|---|---|---|
| Readme | TEXT | 1.66 kB | 2015-04-09 | MD5 checksum: 445ad42882cf90b4c4217b631d493ae9 |
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| the ISA-tab archive of metadata associated with the Chimpanzee transcriptome sequence | ISA-Tab | zip | 4.83 kB | 2015-05-28 | MD5 checksum: 346aecc6151a6292bc2be1e67480eaf8 |
| Date | Action |
|---|---|
| April 27, 2015 | Dataset publish |
| April 27, 2015 | Description updated from : 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. |
| April 27, 2015 | Description updated from : 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. |
| May 28, 2015 | Additional file chimpanzee_transcriptome_ISA.zip added |
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