Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613–619 (2008).
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).
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C. & Raha, D. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008).
Wang, E. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).
Denoeud, F. et al. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 9, R175 (2008).
Maher, C. et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 458, 97–101 (2009).
Marioni, J., Mason, C., Mane, S., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509–1517 (2008).
Hiller, D., Jiang, H., Xu, W. & Wong, W. Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics 25, 3056–3059 (2009).
Jiang, H. & Wong, W.H. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25, 1026–1032 (2009).
Li, B., Ruotti, V., Stewart, R.M., Thomson, J.A. & Dewey, C.N. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26, 493–500 (2010).
Mortazavi, A., Williams, B., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).
Pepke, S., Wold, B. & Mortazavi, A. Computation for ChIP-Seq and RNA-Seq studies. Nat. Methods 6, S22–S32 (2009).
Yaffe, D. & Saxel, O. A myogenic cell line with altered serum requirements for differentiation. Differentiation 7, 159–166 (1977).
Yun, K. & Wold, B. Skeletal muscle determination and differentiation: story of a core regulatory network and its context. Curr. Opin. Cell Biol. 8, 877–889 (1996).
Tapscott, S.J. The circuitry of a master switch: Myod and the regulation of skeletal muscle gene transcription. Development 132, 2685–2695 (2005).
Trapnell, C., Pachter, L. & Salzberg, S. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).
Haas, B.J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).
Eriksson, N. et al. Viral population estimation using pyrosequencing. PLOS Comput. Biol. 4, e1000074 (2008).
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009).
Cordes, K.R. et al. miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460, 705–710 (2009).
Lareau, L.F., Inada, M., Green, R.E., Wengrod, J.C. & Brenner, S.E. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446, 926–929 (2007).
Bullard, J., Purdom, E., Hansen, K., Durinck, S. & Dudoit, S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11, 94 (2010).
Endo, T. & Nadal-Ginard, B. Transcriptional and posttranscriptional control of c-myc during myogenesis: its mRNA remains inducible in differentiated cells and does not suppress the differentiated phenotype. Mol. Cell. Biol. 6, 1412–1421 (1986).
Fuglede, B. & Topsøe, F. in Proceedings of the IEEE International Symposium on Information Theory, 31 (2004).
Cottle, D.L., McGrath, M.J., Cowling, B.S. & Coghill, I.D. FHL3 binds MyoD and negatively regulates myotube formation. J. Cell Sci. 120, 1423–1435 (2007).
Sammeth, M., Lacroix, V., Ribeca, P. & Guigó, R. The FLUX Simulator. < http://flux.sammeth.net >.
Johnson, D., Mortazavi, A., Myers, R. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).