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

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

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Trapnell, Cole, Williams, Brian A, Pertea, Geo, Mortazavi, Ali, Kwan, Gordon, van Baren, Marijke J, Salzberg, Steven L, Wold, Barbara J, Pachter, Lior·2010·Nature Biotechnology

DOI 10.1038/nbt.1621PMC PMC3146043

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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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The Sequence Alignment/Map format and SAMtools
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Alternative isoform regulation in human tissue transcriptomes
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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
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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
ORCID: Trapnell, Cole
Williams, Brian A
Pertea, Geo
Mortazavi, Ali
Salzberg, Steven L
Wold, Barbara J
Pachter, Lior
Venue: Nature Biotechnology
Publisher: Springer Science and Business Media LLC
Published: 2010-05
Volume: 28
Issue: 5
Pages: 511-515
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/nbt.1621
PMC: PMC3146043
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: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
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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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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