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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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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Self-citationMapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Self-citationRNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Self-citationDerrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,135
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853
Cabili, M. N., Trapnell, C., Goff, L. A., Koziol, M. J., Tazón‐Vega, B., Regev, A., & Rinn, J. L. (2011) · Genes & Development · doi:10.1101/gad.17446611 · Cited by 3,551
Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps
Chi, S. W., Zang, J. B., Mele, A., & Darnell, R. B. (2009) · Nature · doi:10.1038/nature08170 · Cited by 1,791
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · cited 2×
“These include methods to study RNA species that are ribosome bound (3), nuclear (4), implicated in RNA editing (5), functional noncoding RNAs (6), in protein–RNA binding sites (7), and interacting in microRNA–mRNA complexes (8).”
MethodMapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., He, X., Mieczkowski, P., Grimm, S. A., Perou, C. M., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq622 · Cited by 1,193
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
Pruitt, K. D., Tatusova, T., Brown, G. R., & Maglott, D. R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1079 · Cited by 1,149
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
English, A. C., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D. M., Reid, J. G., Worley, K. C., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047768 · Cited by 868
Fast and reliable prediction of noncoding RNAs
Stefan Washietl, A., Hofacker, I. L., & Stadler, P. F. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409169102 · Cited by 658
GENCODE: producing a reference annotation for ENCODE
Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C.-K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., et al. (2006) · Genome Biology · doi:10.1186/gb-2006-7-s1-s4 · Cited by 648
Flicek, P., Amode, M. R., Barrell, D. G., Beal, K. M., Brent, S., Chen, Y., Clapham, P., Coates, G. M. P., Fairley, S., Fitzgerald, S. F., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1064 · Cited by 607
Hsu, F., Kent, W. J., Clawson, H., Kuhn, R. M., Diekhans, M., & Haussler, D. H. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl048 · Cited by 503
Statistical inferences for isoform expression in RNA-Seq
Jiang, H., & Wong, W. H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp113 · Cited by 468
Self-citationWidespread RNA and DNA Sequence Differences in the Human Transcriptome
Li, M., Wang, I. X., Li, Y., Bruzel, A., Richards, A. L., Toung, J. M., & Cheung, V. G. (2011) · Science · doi:10.1126/science.1207018 · Cited by 462
Adams, M. D., Soares, M. B., Kerlavage, A. R., Fields, C., & Venter, J. C. (1993) · Nature Genetics · doi:10.1038/ng0893-373 · Cited by 358
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
Au, K. F., Jiang, H., Lin, L., Xing, Y., & Wong, W. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq211 · Cited by 341
Self-citationImproving PacBio Long Read Accuracy by Short Read Alignment
Au, K. F., Underwood, J. G., Lee, L., & Wong, W. H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046679 · Cited by 335
Self-citationRNAz 2.0: improved noncoding RNA detection.
Gruber, A. R., Findeiß, S., Stefan Washietl, A., Hofacker, I. L., & Stadler, P. F. (2010) · PubMed · Cited by 237
Structured RNAs in the ENCODE selected regions of the human genomePreprint
Stefan Washietl, A., Pedersen, J. S., Korbel, J. O., Stocsits, C., Gruber, A. R., Hackermüller, J., Jana Hertel, A., Marz, M., Reiche, K., Andrea Tanzer, A., et al. (2007) · Genome Research · doi:10.1101/gr.5650707 · Cited by 178
Stefan Washietl, A., & Hofacker, I. L. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.018 · Cited by 160
Li, J. J., Jiang, C., Brown, J., Huang, H., & Bickel, P. J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113972108 · Cited by 140
Miura, T., Luo, Y., Khrebtukova, I., Brandenberger, R., Zhou, D., Thies, R. S., Vasicek, T., Young, H. Y., LEBKOWSKI, J. S., Carpenter, M. K., et al. (2004) · Stem Cells and Development · doi:10.1089/scd.2004.13.694 · Cited by 94
Identifiability of isoform deconvolution from junction arrays and RNA-Seq
Hiller, D. J., Jiang, H., Xu, W., & Wong, W. H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp544 · Cited by 65
Self-citationRederstorff, M., Bernhart, S. H., Andrea Tanzer, A., Żywicki, M., Perfler, K., Lukasser, M., Hofacker, I. L., & Hüttenhofer, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq057 · Cited by 46
Nuclear RNA Sequencing of the Mouse Erythroid Cell Transcriptome
Mitchell, J. A., Clay, I., Umlauf, D., Chen, C., Moir, C. A., Eskiw, C. H., Schoenfelder, S., Chakalova, L., Nagano, T., & Fraser, P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049274 · Cited by 34
Simultaneous Isoform Discovery and Quantification from RNA-Seq
Hiller, D. J., & Wong, W. H. (2012) · Statistics in Biosciences · doi:10.1007/s12561-012-9069-2 · Cited by 20
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A survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794
Opportunities and challenges in long-read sequencing data analysis
Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530
PacBio Sequencing and its Applications
Rhoads, A., & Au, K. F. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.08.002 · Cited by 2,488
Self-citationTranscriptome assembly from long-read RNA-seq alignments with StringTie2
Kovaka, S., Zimin, A. V., Pertea, G. M., Razaghi, R., Salzberg, S. L., & Pertea, M. (2019) · Genome biology · doi:10.1186/s13059-019-1910-1 · Cited by 2,041
RNA sequencing: the teenage years
Stark, R., Grzelak, M., & Hadfield, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0150-2 · Cited by 2,041
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
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