De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences.
De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences.
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DOI：
10.1186/s13742-015-0061-x
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发表时间：
2015
期刊：
影响因子：
9.2
通讯作者：
Norgren RB Jr
中科院分区：
文献类型：
--
作者：
Maudhoo MD;Madison JD;Norgren RB Jr
普通黑猩猩（Pan troglodytes）和倭黑猩猩（Pan paniscus）是与人类关系最密切的物种。因此，获得完整准确的黑猩猩核苷酸和蛋白质序列对于了解人类如何进化出独特的能力尤为重要。我们提供的转录组数据来自四个未转化的细胞类型，从参考Pan troglodytes，“克林特”，更好地注释黑猩猩基因组，并提供经验验证这个重要物种的基因模型。从四种组织培养的原代细胞中提取RNA：皮肤、脂肪基质、血管平滑肌和骨骼肌。这四个RNA样品在Illumina HiSeq 2000平台上测序。将序列保藏在国家生物技术信息中心（NCBI）序列读取档案（SRA）中。将转录物组装、注释并保存在NCBI转录组鸟枪组装（TSA）数据库中。我们已经提供了44，275个转录本的高质量注释和全长编码序列（CDS）。这个集合代表了总共10，110个独特的基因，从而为它们的存在提供了经验支持。该数据集可用于改进黑猩猩基因组的注释。本文的在线版本（doi：10.1186/s13742-015-0061-x）包含补充材料，可供授权用户使用。
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 National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). Transcripts were assembled, annotated and deposited in the NCBI 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 the annotation of the Pan troglodytes genome. The online version of this article (doi:10.1186/s13742-015-0061-x) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/bts094
发表时间：
2012-04-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Schulz MH;Zerbino DR;Vingron M;Birney E
通讯作者：
Birney E
影响因子：
30.8
作者：
GISH, W;STATES, DJ
通讯作者：
STATES, DJ
影响因子：
2.5
作者：
Wall, Jeffrey D.
通讯作者：
Wall, Jeffrey D.
影响因子：
7
作者：
Zerbino, Daniel R.;Birney, Ewan
通讯作者：
Birney, Ewan
影响因子：
12.3
作者：
Wetterbom, Anna;Ameur, Adam;Cavelier, Lucia
通讯作者：
Cavelier, Lucia