Cited by 15,556Genomics and Phylogenetic StudiesRNA Research and SplicingSingle-cell and spatial transcriptomics

The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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Abstract

High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes. These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.

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  1. Mortazavi, A., Williams, B., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008). · DOI · Paper page
  2. Fuglede, B. & Topsøe, F. in Proceedings of the IEEE International Symposium on Information Theory, 31 (2004).

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Metadata

Authors
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L.
Affiliations
  • University of Maryland, College Park (US)
  • California Institute of Technology (US)
  • University of California, Berkeley (US)
Corresponding author
Pachter, Lior
Venue
Nature Biotechnology
Published
2010-05
Volume
28
Issue
5
Pages
511-515
ISSN
  • 0733-222X (ISSN-L)
  • 1087-0156
  • 1546-1696
OpenAlex
W2141458291
Cited by
15,556
References
31
Citations by year
2026: 449 · 2025: 708 · 2024: 865 · 2023: 1081 · 2022: 1349 · 2021: 1458 · 2020: 1444 · 2019: 1349 · 2018: 1319 · 2017: 1225 · 2016: 1051 · 2015: 936 · 2014: 889 · 2013: 684 · 2012: 447
FWCI
185.65
Type
journal article
Language
en
Open access
Locations
  • Nature Biotechnology (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • CaltechAUTHORS (California Institute of Technology) (submittedVersion)
Funders
  • National Human Genome Research Institute (U54HG004576, R01HG006102)
  • National Institute of General Medical Sciences (R01GM083873)
  • U.S. National Library of Medicine (R01LM006845)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords
transcript assembly, transcript quantification, Cufflinks, unannotated transcripts, isoform switching, alternative splicing, alternative transcription, cell differentiation, myogenesis, genome annotation
MeSH terms
Algorithms, Animals, Cell Differentiation, Cell Line, RNA, Messenger, Software, Proto-Oncogene Proteins c-myc, Genome, Sequence Analysis, RNA, Protein Isoforms, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Mice

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