Cited by 358Genomics and Phylogenetic StudiesRNA Research and SplicingSingle-cell and spatial transcriptomics

Characterization of the human ESC transcriptome by hybrid sequencing

Open access
Au, Kin Fai, Sebastiano, Vittorio, Afshar, Pegah Tootoonchi, Durruthy, Jens Durruthy, Lee, Lawrence, Williams, Brian A., van Bakel, Harm, Schadt, Eric E. +3 more·2013·Proceedings of the National Academy of Sciences

Abstract

Significance: Isoform identification and discovery are an important goal for transcriptome analysis because the majority of human genes express multiple isoforms with context- and tissue-specific functions. Better annotation of isoforms will also benefit downstream analysis such as expression quantification. Current RNA-Seq methods based on short-read sequencing are not reliable for isoform discovery. In this study we developed a new method based on the combined analysis of short reads and long reads generated, respectively, by second- and third-generation sequencing and applied this method to obtain a comprehensive characterization of the transcriptome of the human embryonic stem cell. The results showed that large gain in sensitivity and specificity can be achieved with this strategy.

Integrity signals

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Crossref · 10.1073/pnas.1320101110

Cites

33 of 33 references verified0 citation errors · 0 not checkable

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  • PacBio RNA-seq has proven useful for unraveling isoform diversity at complex loci and for determining allele-specific expression from single reads.

    “The technology has proven useful for unraveling isoform diversity at complex loci [186], and for determining allele-specific expression from single reads [187].”

    From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [186]

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Authors
Au, K. F., Sebastiano, V., Afshar, P. T., Durruthy, J. D., Lee, L., Williams, B. A., van Bakel, H., Schadt, E. E., Reijo-Pera, R. A., Underwood, J. G., & Wong, W. H.
Affiliations
  • Stanford University (US)
  • Stanford Medicine (US)
  • Center for Human Pluripotent Stem Cell Research and Education, Department of Obstetrics and Gynecology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305;
  • Invitae (United States) (US)
  • California Institute of Technology (US)
  • Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029-6574; and
  • Icahn School of Medicine at Mount Sinai (US)
  • University of Washington (US)
Venue
Proceedings of the National Academy of Sciences
Published
2013-11-26
Volume
110
Issue
50
Pages
E4821-30
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
OpenAlex
W2054841963
Cited by
341
References
34
Citations by year
2026: 8 · 2025: 8 · 2024: 19 · 2023: 17 · 2022: 34 · 2021: 49 · 2020: 33 · 2019: 48 · 2018: 28 · 2017: 31 · 2016: 24 · 2015: 21 · 2014: 19 · 2012: 1
FWCI
9.56
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • CaltechAUTHORS (California Institute of Technology) (submittedVersion)
Funders
  • National Heart, Lung, and Blood Institute (U01HL100397)
  • National Human Genome Research Institute (U54HG004576, R01HG005717, U54HG006998)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD068158)
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
human embryonic stem cells, transcriptome, isoform identification, novel transcripts, pluripotency genes, gene expression profiling, hybrid sequencing, transcriptome completeness
MeSH terms
Humans, Male, Alternative Splicing, Protein Isoforms, Gene Expression Profiling, Embryonic Stem Cells, High-Throughput Nucleotide Sequencing, Transcriptome

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

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