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Characterization of the human ESC transcriptome by hybrid sequencing
Open accessAbstract
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.
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“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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Metadata
- 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
- Publisher
- National Academy of Sciences
- Published
- 2013-11-26
- Volume
- 110
- Issue
- 50
- Pages
- E4821-30
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3864310
- 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
- FWCI
- 9.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- 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
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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