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

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Characterization of the human ESC transcriptome by hybrid sequencing

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Au, Kin Fai, Sebastiano, Vittorio, Afshar, Pegah Tootoonchi, Durruthy, Jens Durruthy, Lee, Lawrence, Williams, Brian A., van Bakel, Harm, Schadt, Eric E., Reijo-Pera, Renee A., Underwood, Jason G., Wong, Wing Hung·2013·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.1320101110PMC PMC3864310

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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.

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Additional file 11 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 14 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 12 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 16 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 13 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 7 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 1 of Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings
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Additional file 4 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 9 of Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
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Additional file 8 of Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
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Additional file 5 of Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
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Additional file 2 of Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
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Additional file 17 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 7 of Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
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Additional file 2 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 3 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 4 of Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
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Additional file 1 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 9 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 18 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 5 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 4 of Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
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Additional file 8 of Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica
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Additional file 3 of Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
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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)
ORCID: Au, Kin Fai
Sebastiano, Vittorio
Williams, Brian A.
Schadt, Eric E.
Wong, Wing Hung
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
DOI: 10.1073/pnas.1320101110
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

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Characterization of the human ESC transcriptome by hybrid sequencing

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