메뉴 건너뛰기




Volumn 9, Issue 5, 2014, Pages 989-1009

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLINICAL PROTOCOL; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE LIBRARY; GENE TARGETING; GENE TECHNOLOGY; GENETIC VARIABILITY; HUMAN; HUMAN CELL; LIMIT OF QUANTITATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA CAPTURE SEQUENCING; RNA PROBE; RNA SEQUENCE; RNA SPLICING; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; COMPUTER PROGRAM; EXON; GENETIC ASSOCIATION; GENETICS; NUCLEIC ACID AMPLIFICATION; OLIGONUCLEOTIDE PROBE; PROCEDURES;

EID: 84899561113     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.058     Document Type: Article
Times cited : (136)

References (48)
  • 2
    • 46249103973 scopus 로고    scopus 로고
    • Stem cell transcriptome profiling via massive-scale mRNA sequencing
    • Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613-619 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 613-619
    • Cloonan, N.1
  • 3
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of rna-seq experiments with top hat and cufflinks
    • Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 4
    • 80052960863 scopus 로고    scopus 로고
    • Next-generation transcriptome assembly
    • Martin, J.A. & Wang, Z. Next-generation transcriptome assembly. Nat. Rev. Genet. 12, 671-682 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 671-682
    • Martin, J.A.1    Wang, Z.2
  • 5
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • Ozsolak, F. & Milos, P.M. RNA sequencing: Advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 6
    • 80052521697 scopus 로고    scopus 로고
    • Synthetic spike-in standards for RNA-seq experiments
    • Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543-1551 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1543-1551
    • Jiang, L.1
  • 7
    • 84855539848 scopus 로고    scopus 로고
    • Targeted RNA sequencing reveals the deep complexity of the human transcriptome
    • Mercer, T.R. et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 30, 99-104 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 99-104
    • Mercer, T.R.1
  • 8
    • 75349100601 scopus 로고    scopus 로고
    • Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
    • 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).
    • (2009) Genome Biol. , vol.10
    • Levin, J.Z.1
  • 9
    • 68349089152 scopus 로고    scopus 로고
    • Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
    • Zhang, K. et al. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat. Methods 6, 613-618 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 613-618
    • Zhang, K.1
  • 10
    • 66349122954 scopus 로고    scopus 로고
    • Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    • Li, J.B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210-1213 (2009).
    • (2009) Science , vol.324 , pp. 1210-1213
    • Li, J.B.1
  • 11
    • 80054757012 scopus 로고    scopus 로고
    • Performance comparison of exome DNA sequencing technologies
    • Clark, M.J. et al. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 29, 908-914 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 908-914
    • Clark, M.J.1
  • 12
    • 77956340995 scopus 로고    scopus 로고
    • Comprehensive comparative analysis of strand-specific RNA sequencing methods
    • Levin, J.Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 709-715
    • Levin, J.Z.1
  • 14
    • 77449121614 scopus 로고    scopus 로고
    • Target-enrichment strategies for next-generation sequencing
    • Mamanova, L. et al. Target-enrichment strategies for next-generation sequencing. Nat. Methods 7, 111-118 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 111-118
    • Mamanova, L.1
  • 15
    • 53249132629 scopus 로고    scopus 로고
    • Identification of genetic variants using bar-coded multiplexed sequencing
    • Craig, D.W. et al. Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods 5, 887-893 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 887-893
    • Craig, D.W.1
  • 16
    • 84865728918 scopus 로고    scopus 로고
    • Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
    • 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).
    • (2012) Genome Res. , vol.22 , pp. 1698-1710
    • Howald, C.1
  • 17
    • 35748953750 scopus 로고    scopus 로고
    • Multiplex amplification of large sets of human exons
    • Porreca, G.J. et al. Multiplex amplification of large sets of human exons. Nat. Methods 4, 931-936 (2007).
    • (2007) Nat. Methods , vol.4 , pp. 931-936
    • Porreca, G.J.1
  • 18
    • 27244436950 scopus 로고    scopus 로고
    • Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments
    • 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).
    • (2005) Nucleic Acids Res. , vol.33
    • Dahl, F.1    Gullberg, M.2    Stenberg, J.3    Landegren, U.4    Nilsson, M.5
  • 19
    • 84883364264 scopus 로고    scopus 로고
    • Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
    • Anders, S. et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. 8, 1765-1786 (2013).
    • (2013) Nat. Protoc. , vol.8 , pp. 1765-1786
    • Anders, S.1
  • 21
    • 33748645500 scopus 로고    scopus 로고
    • GENCODE: Producing a reference annotation for ENCODE
    • S4
    • Harrow, J. et al. GENCODE: Producing a reference annotation for ENCODE. Genome Biol. 7 (suppl. 1), S4: 1-9 (2006).
    • (2006) Genome Biol. , vol.7 , Issue.1 , pp. 1-9
    • Harrow, J.1
  • 22
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
    • Dunham, I.1
  • 23
    • 81855178276 scopus 로고    scopus 로고
    • Somatic retrotransposition alters the genetic landscape of the human brain
    • Baillie, J.K. et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479, 534-537 (2011).
    • (2011) Nature , vol.479 , pp. 534-537
    • Baillie, J.K.1
  • 24
    • 27844529344 scopus 로고    scopus 로고
    • Proposed methods for testing and selecting the ERCC external RNA controls
    • ERC Consortium.
    • ERC Consortium. Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6, 150 (2005).
    • (2005) BMC Genomics , vol.6 , pp. 150
  • 25
    • 84855295457 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    • Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).
    • (2012) Nucleic Acids Res. , vol.40
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 26
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 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).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 27
    • 84865527768 scopus 로고    scopus 로고
    • Detecting differential usage of exons from RNA-seq data
    • Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008-2017 (2012).
    • (2012) Genome Res. , vol.22 , pp. 2008-2017
    • Anders, S.1    Reyes, A.2    Huber, W.3
  • 28
    • 84861743958 scopus 로고    scopus 로고
    • RNA-SeQC: RNA-seq metrics for quality control and process optimization
    • DeLuca, D.S. et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28, 1530-1532 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1530-1532
    • Deluca, D.S.1
  • 29
    • 33646361583 scopus 로고    scopus 로고
    • Gene pattern 2.0
    • Reich, M. et al. GenePattern 2.0. Nat. Genet. 38, 500-501 (2006).
    • (2006) Nat. Genet. , vol.38 , pp. 500-501
    • Reich, M.1
  • 30
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • 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).
    • (2010) Genome Biol. , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 31
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
    • (2013) Genome Biol. , vol.14
    • Kim, D.1
  • 32
    • 77649235913 scopus 로고    scopus 로고
    • How to do successful gene expression analysis using real-Time PCR
    • Derveaux, S., Vandesompele, J. & Hellemans, J. How to do successful gene expression analysis using real-Time PCR. Methods 50, 227-230 (2010).
    • (2010) Methods , vol.50 , pp. 227-230
    • Derveaux, S.1    Vandesompele, J.2    Hellemans, J.3
  • 33
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 34
    • 84871809302 scopus 로고    scopus 로고
    • STAR: Ultrafast universal RNA-seq aligner
    • Dobin, A. et al. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 15-21
    • Dobin, A.1
  • 35
    • 77955443472 scopus 로고    scopus 로고
    • Detection of splice junctions from paired-end RNA-seq data by SpliceMap
    • 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).
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4570-4578
    • Au, K.F.1    Jiang, H.2    Lin, L.3    Xing, Y.4    Wong, W.H.5
  • 36
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-Tolerant detection of complex variants and splicing in short reads
    • Wu, T.D. & Nacu, S. Fast and SNP-Tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 37
    • 84872198346 scopus 로고    scopus 로고
    • Differential analysis of gene regulation at transcript resolution with RNA-seq
    • Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46-53 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 46-53
    • Trapnell, C.1
  • 38
    • 84874597027 scopus 로고    scopus 로고
    • IReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data
    • Mezlini, A.M. et al. iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res. 23, 519-529 (2013).
    • (2013) Genome Res. , vol.23 , pp. 519-529
    • Mezlini, A.M.1
  • 39
    • 84055216924 scopus 로고    scopus 로고
    • Sparse linear modeling of next-generation mRNA sequencing (RNA-seq) data for isoform discovery and abundance estimation
    • 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).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 19867-19872
    • Li, J.J.1    Jiang, C.R.2    Brown, J.B.3    Huang, H.4    Bickel, P.J.5
  • 40
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and samtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 41
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R. & Hall, I.M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 42
    • 58149178565 scopus 로고    scopus 로고
    • The ucsc genome browser database: Update 2009
    • Kuhn, R.M. et al. The UCSC Genome Browser Database: Update 2009. Nucleic Acids Res. 37, D755-761 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Kuhn, R.M.1
  • 44
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • 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).
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1
  • 45
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
    • (2012) Nature , vol.489 , pp. 101-108
    • Djebali, S.1
  • 46
    • 84879692466 scopus 로고    scopus 로고
    • Comparative analysis of RNA sequencing methods for degraded or low-input samples
    • Adiconis, X. et al. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat. Methods 10, 623-629 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 623-629
    • Adiconis, X.1
  • 47
    • 84861115379 scopus 로고    scopus 로고
    • Comprehensive qPCR profiling of gene expression in single neuronal cells
    • 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).
    • (2012) Nat. Protoc. , vol.7 , pp. 118-127
    • Citri, A.1    Pang, Z.P.2    Sudhof, T.C.3    Wernig, M.4    Malenka, R.C.5
  • 48
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • 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).
    • (2012) Genome Res. , vol.22 , pp. 1775-1789
    • Derrien, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.