Targeted sequencing for gene discovery and quantification using RNA CaptureSeq (original) (raw)

• 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).
  Article CAS Google Scholar
• Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613–619 (2008).
  Article CAS Google Scholar
• Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).
  Article CAS Google Scholar
• Martin, J.A. & Wang, Z. Next-generation transcriptome assembly. Nat. Rev. Genet. 12, 671–682 (2011).
  Article CAS Google Scholar
• Ozsolak, F. & Milos, P.M. RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87–98 (2011).
  Article CAS Google Scholar
• Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543–1551 (2011).
  Article CAS Google Scholar
• Mercer, T.R. et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 30, 99–104 (2012).
  Article CAS Google Scholar
• Levin, J.Z. et al. Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol. 10, R115 (2009).
  Article Google Scholar
• Zhang, K. et al. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat. Methods 6, 613–618 (2009).
  Article CAS Google Scholar
• Li, J.B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210–1213 (2009).
  Article CAS Google Scholar
• Clark, M.J. et al. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 29, 908–914 (2011).
  Article CAS Google Scholar
• Levin, J.Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709–715 (2010).
  Article CAS Google Scholar
• Turner, E.H., Ng, S.B., Nickerson, D.A. & Shendure, J. Methods for genomic partitioning. Annu. Rev. Genomics Hum. Genet. 10, 263–284 (2009).
  Article CAS Google Scholar
• Mamanova, L. et al. Target-enrichment strategies for next-generation sequencing. Nat. Methods 7, 111–118 (2010).
  Article CAS Google Scholar
• Craig, D.W. et al. Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods 5, 887–893 (2008).
  Article CAS Google Scholar
• Howald, C. et al. Combining RT-PCR–seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res. 22, 1698–1710 (2012).
  Article CAS Google Scholar
• Porreca, G.J. et al. Multiplex amplification of large sets of human exons. Nat. Methods 4, 931–936 (2007).
  Article CAS Google Scholar
• Dahl, F., Gullberg, M., Stenberg, J., Landegren, U. & Nilsson, M. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res. 33, e71 (2005).
  Article Google Scholar
• Anders, S. et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. 8, 1765–1786 (2013).
  Article Google Scholar
• Kreil, D.P., Russell, R.R. & Russell, S. Microarray oligonucleotide probes. Methods Enzymol. 410, 73–98 (2006).
  Article CAS Google Scholar
• Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7 (suppl. 1), S4: 1–9 (2006).
  PubMed Google Scholar
• Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
  Article CAS Google Scholar
• Baillie, J.K. et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479, 534–537 (2011).
  Article CAS Google Scholar
• ERC Consortium. Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6, 150 (2005).
• Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).
  Article CAS Google Scholar
• Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
  Article CAS Google Scholar
• Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008–2017 (2012).
  Article CAS Google Scholar
• DeLuca, D.S. et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28, 1530–1532 (2012).
  Article CAS Google Scholar
• Reich, M. et al. GenePattern 2.0. Nat. Genet. 38, 500–501 (2006).
  Article CAS Google Scholar
• Goecks, J., Nekrutenko, A. & Taylor, J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
  Article Google Scholar
• Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
  Article Google Scholar
• Derveaux, S., Vandesompele, J. & Hellemans, J. How to do successful gene expression analysis using real-time PCR. Methods 50, 227–230 (2010).
  Article CAS Google Scholar
• Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
  Article CAS Google Scholar
• Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
  Article CAS Google Scholar
• Au, K.F., Jiang, H., Lin, L., Xing, Y. & Wong, W.H. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 38, 4570–4578 (2010).
  Article CAS Google Scholar
• Wu, T.D. & Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873–881 (2010).
  Article CAS Google Scholar
• Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46–53 (2013).
  Article CAS Google Scholar
• Mezlini, A.M. et al. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res. 23, 519–529 (2013).
  Article CAS Google Scholar
• Li, J.J., Jiang, C.R., Brown, J.B., Huang, H. & Bickel, P.J. Sparse linear modeling of next-generation mRNA sequencing (RNA-seq) data for isoform discovery and abundance estimation. Proc. Natl. Acad. Sci. USA 108, 19867–19872 (2011).
  Article CAS Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article Google Scholar
• Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
  Article CAS Google Scholar
• Kuhn, R.M. et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37, D755–761 (2009).
  Article CAS Google Scholar
• Amaral, P.P., Clark, M.B., Gascoigne, D.K., Dinger, M.E. & Mattick, J.S. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 39, D146–D151 (2011).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101–108 (2012).
  Article CAS Google Scholar
• Adiconis, X. et al. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat. Methods 10, 623–629 (2013).
  Article CAS Google Scholar
• Citri, A., Pang, Z.P., Sudhof, T.C., Wernig, M. & Malenka, R.C. Comprehensive qPCR profiling of gene expression in single neuronal cells. Nat. Protoc. 7, 118–127 (2012).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar