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- Publisher Website: 10.1038/s41467-023-42636-1
- Scopus: eid_2-s2.0-85176230028
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Article: CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data
Title | CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data |
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Authors | |
Issue Date | 9-Nov-2023 |
Publisher | Nature Research |
Citation | Nature Communications, 2023, v. 14, n. 1 How to Cite? |
Abstract | Five-prime single-cell RNA-seq (scRNA-seq) has been widely employed to profile cellular transcriptomes, however, its power of analysing transcription start sites (TSS) has not been fully utilised. Here, we present a computational method suite, CamoTSS, to precisely identify TSS and quantify its expression by leveraging the cDNA on read 1, which enables effective detection of alternative TSS usage. With various experimental data sets, we have demonstrated that CamoTSS can accurately identify TSS and the detected alternative TSS usages showed strong specificity in different biological processes, including cell types across human organs, the development of human thymus, and cancer conditions. As evidenced in nasopharyngeal cancer, alternative TSS usage can also reveal regulatory patterns including systematic TSS dysregulations. |
Persistent Identifier | http://hdl.handle.net/10722/339955 |
ISSN | 2023 Impact Factor: 14.7 2023 SCImago Journal Rankings: 4.887 |
DC Field | Value | Language |
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dc.contributor.author | Hou, Ruiyan | - |
dc.contributor.author | Hon, Chung-Chau | - |
dc.contributor.author | Huang, Yuanhua | - |
dc.date.accessioned | 2024-03-11T10:40:35Z | - |
dc.date.available | 2024-03-11T10:40:35Z | - |
dc.date.issued | 2023-11-09 | - |
dc.identifier.citation | Nature Communications, 2023, v. 14, n. 1 | - |
dc.identifier.issn | 2041-1723 | - |
dc.identifier.uri | http://hdl.handle.net/10722/339955 | - |
dc.description.abstract | <p>Five-prime single-cell RNA-seq (scRNA-seq) has been widely employed to profile cellular transcriptomes, however, its power of analysing transcription start sites (TSS) has not been fully utilised. Here, we present a computational method suite, CamoTSS, to precisely identify TSS and quantify its expression by leveraging the cDNA on read 1, which enables effective detection of alternative TSS usage. With various experimental data sets, we have demonstrated that CamoTSS can accurately identify TSS and the detected alternative TSS usages showed strong specificity in different biological processes, including cell types across human organs, the development of human thymus, and cancer conditions. As evidenced in nasopharyngeal cancer, alternative TSS usage can also reveal regulatory patterns including systematic TSS dysregulations.<br></p> | - |
dc.language | eng | - |
dc.publisher | Nature Research | - |
dc.relation.ispartof | Nature Communications | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.title | CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data | - |
dc.type | Article | - |
dc.identifier.doi | 10.1038/s41467-023-42636-1 | - |
dc.identifier.scopus | eid_2-s2.0-85176230028 | - |
dc.identifier.volume | 14 | - |
dc.identifier.issue | 1 | - |
dc.identifier.eissn | 2041-1723 | - |
dc.identifier.issnl | 2041-1723 | - |