Erratum: A single-molecule long-read survey of the human transcriptome (Nat. Biotechnol. (2013) 31 (1009-1014) DOI: 10.1038/nbt.2705);A single-molecule long-read survey of the human transcriptome

Nature Biotechnology

Volumn 31, Issue 11, 2013, Pages 1009-1014

  Sharon, Donald ^a,b   Tilgner, Hagen ^a   Grubert, Fabian ^a   Snyder, Michael ^a  

^a STANFORD UNIVERSITY   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAPPING; NUCLEIC ACIDS;

BIOLOGICAL PROCESS; HIGH CONFIDENCE; HUMAN ORGANS; NON-CODING RNAS; RNA MOLECULES; SINGLE MOLECULE; SINGLE MOLECULE LEVEL; TRANSCRIPTOMES;

RNA;

COMPLEMENTARY DNA; LONG UNTRANSLATED RNA; NUCLEOTIDE; POLYADENYLATED RNA; TRANSCRIPTOME;

ARTICLE; DNA SEQUENCE; GENE EXPRESSION; GENE MAPPING; GENE STRUCTURE; HUMAN; HUMAN TISSUE; INTRON; PRIORITY JOURNAL; RNA SEQUENCE; TRANSCRIPTION INITIATION SITE;

EUKARYOTA;

DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; HUMANS; INTRONS; MARKOV CHAINS; RNA, MESSENGER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84887412533     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt0314-291b     Document Type: Erratum

References (27)

1. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349 (2008).
2. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008).
3. Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-960 (2008).
4. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).
5. Wilhelm, B.T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239-1243 (2008).
6. Wang, Z., Gerstein, M. & Snyder, M. RNA-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63 (2009).
7. Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
8. Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
9. Quail, M.A. et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13, 341 (2012).
10. Koren, S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30, 693-700 (2012).
11. Au, K.F., Underwood, J.G., Lee, L. & Wong, W.H. Improving PacBio long read accuracy by short read alignment. PLoS ONE 7, e46679 (2012).
12. Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012).
13. Travers, K.J., Chin, C.S., Rank, D.R., Eid, J.S. & Turner, S.W. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res. 38, e159 (2010).
14. Tilgner, H. et al. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda) 3, 387-397 (2013).
15. Wu, T.D. & Watanabe, C.K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875 (2005).
16. R Development Core Team. R: A language and environment for statistical computing http://www.R-project.org/(R Foundation for Statistical Computing, Vienna, Austria, 2012).
17. van Bakel, H., Nislow, C., Blencowe, B.J. & Hughes, T.R. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 8, e1000371 (2010).
18. Daley, T. & Smith, A.D. Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325-327 (2013).
19. Pickrell, J.K., Pai, A.A., Gilad, Y. & Pritchard, J.K. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet. 6, e1001236 (2010).
20. Fagnani, M. et al. Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol. 8, R108 (2007).
21. Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789 (2012).
22. Parra, G., Blanco, E. & Guigó, R. GeneID in Drosophila. Genome Res. 10, 511-515 (2000).
23. Eyras, E., Caccamo, M., Curwen, V. & Clamp, M. ESTGenes: alternative splicing from ESTs in Ensembl. Genome Res. 14, 976-987 (2004).
24. Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
25. Gingeras, T. Missing lincs in the transcriptome. Nat. Biotechnol. 27, 346-347 (2009).
26. Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
27. Himmelmann, L. & R Development Core Team. R: A language and environment for statistical computing http://cran.r-project.org/web/packages/ HMM/HMM.pdf (R Foundation for Statistical Computing, Vienna, Austria, 2010).