메뉴 건너뛰기




Volumn 17, Issue 1, 2016, Pages

Classification of low quality cells from single-cell RNA-seq data

Author keywords

[No Author keywords available]

Indexed keywords

BONE MARROW; CD4+ T LYMPHOCYTE; CLASSIFICATION; DENDRITIC CELL; MOUSE EMBRYONIC STEM CELL; RNA SEQUENCE; ANIMAL; BONE MARROW CELL; DNA MICROARRAY; EMBRYONIC STEM CELL; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; MOUSE; NUCLEOTIDE SEQUENCE; SINGLE CELL ANALYSIS;

EID: 84958058589     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-0888-1     Document Type: Article
Times cited : (464)

References (53)
  • 1
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 2
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: advances, challenges and opportunities
    • Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet. 2011;12:87-98.
    • (2011) Nat Rev Genet , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 3
    • 79953288433 scopus 로고    scopus 로고
    • Development and applications of single-cell transcriptome analysis
    • Tang F, Lao K, Surani MA. Development and applications of single-cell transcriptome analysis. Nat Meth. 2011;8:S6-11.
    • (2011) Nat Meth , vol.8 , pp. S6-11
    • Tang, F.1    Lao, K.2    Surani, M.A.3
  • 4
    • 84896739948 scopus 로고    scopus 로고
    • Single cell genomics: advances and future perspectives
    • Macaulay IC, Voet T. Single cell genomics: advances and future perspectives. PLoS Genet. 2014;10:e1004126.
    • (2014) PLoS Genet , vol.10 , pp. e1004126
    • Macaulay, I.C.1    Voet, T.2
  • 5
    • 84897139457 scopus 로고    scopus 로고
    • Every cell is special: genome-wide studies add a new dimension to single-cell biology
    • Junker JP, van Oudenaarden A. Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell. 2014;157:8-11.
    • (2014) Cell , vol.157 , pp. 8-11
    • Junker, J.P.1    Oudenaarden, A.2
  • 6
    • 84901188210 scopus 로고    scopus 로고
    • Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis
    • Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L, Taylor AE, et al. Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis. Cell Reports. 2014;7:1130-42.
    • (2014) Cell Reports , vol.7 , pp. 1130-1142
    • Mahata, B.1    Zhang, X.2    Kolodziejczyk, A.A.3    Proserpio, V.4    Haim-Vilmovsky, L.5    Taylor, A.E.6
  • 8
    • 84903185013 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
    • Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 2014;510:363-9.
    • (2014) Nature , vol.510 , pp. 363-369
    • Shalek, A.K.1    Satija, R.2    Shuga, J.3    Trombetta, J.J.4    Gennert, D.5    Lu, D.6
  • 9
    • 84923292191 scopus 로고    scopus 로고
    • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
    • Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotech. 2015;33:155-60.
    • (2015) Nat Biotech , vol.33 , pp. 155-160
    • Buettner, F.1    Natarajan, K.N.2    Casale, F.P.3    Proserpio, V.4    Scialdone, A.5    Theis, F.J.6
  • 10
    • 84921466417 scopus 로고    scopus 로고
    • Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing
    • Usoskin D, Furlan A, Islam S, Abdo H, Lönnerberg P, Lou D, et al. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nat Neurosci. 2015;18:145-53.
    • (2015) Nat Neurosci , vol.18 , pp. 145-153
    • Usoskin, D.1    Furlan, A.2    Islam, S.3    Abdo, H.4    Lönnerberg, P.5    Lou, D.6
  • 12
    • 84892179132 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
    • Deng Q, Ramskold D, Reinius B, Sandberg R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science. 2014;343:193-6.
    • (2014) Science , vol.343 , pp. 193-196
    • Deng, Q.1    Ramskold, D.2    Reinius, B.3    Sandberg, R.4
  • 14
    • 84883134780 scopus 로고    scopus 로고
    • Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
    • Xue Z, Huang K, Cai C, Cai L, Jiang C-Y, Feng Y, et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature. 2014;500:593-7.
    • (2014) Nature , vol.500 , pp. 593-597
    • Xue, Z.1    Huang, K.2    Cai, C.3    Cai, L.4    Jiang, C.-Y.5    Feng, Y.6
  • 15
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32:381-6.
    • (2014) Nat Biotechnol , vol.32 , pp. 381-386
    • Trapnell, C.1    Cacchiarelli, D.2    Grimsby, J.3    Pokharel, P.4    Li, S.5    Morse, M.6
  • 16
    • 84895562012 scopus 로고    scopus 로고
    • From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing
    • Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res. 2014;24:496-510.
    • (2014) Genome Res , vol.24 , pp. 496-510
    • Marinov, G.K.1    Williams, B.A.2    McCue, K.3    Schroth, G.P.4    Gertz, J.5    Myers, R.M.6
  • 17
    • 84928227321 scopus 로고    scopus 로고
    • Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing
    • Biase FH, Cao X, Zhong S. Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome Res. 2014;24:1787-96.
    • (2014) Genome Res , vol.24 , pp. 1787-1796
    • Biase, F.H.1    Cao, X.2    Zhong, S.3
  • 18
    • 84929684999 scopus 로고    scopus 로고
    • Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
    • Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161:1202-14.
    • (2015) Cell , vol.161 , pp. 1202-1214
    • Macosko, E.Z.1    Basu, A.2    Satija, R.3    Nemesh, J.4    Shekhar, K.5    Goldman, M.6
  • 19
    • 84929684998 scopus 로고    scopus 로고
    • Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
    • Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161:1187-201.
    • (2015) Cell , vol.161 , pp. 1187-1201
    • Klein, A.M.1    Mazutis, L.2    Akartuna, I.3    Tallapragada, N.4    Veres, A.5    Li, V.6
  • 21
    • 84865074382 scopus 로고    scopus 로고
    • RSeQC: quality control of RNA-seq experiments
    • Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012;28:2184-5.
    • (2012) Bioinformatics , vol.28 , pp. 2184-2185
    • Wang, L.1    Wang, S.2    Li, W.3
  • 22
    • 84895069488 scopus 로고    scopus 로고
    • Quantitative single-cell rna-seq with unique molecular identifiers
    • Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. Quantitative single-cell rna-seq with unique molecular identifiers. Nat Meth. 2014;11:163-6.
    • (2014) Nat Meth , vol.11 , pp. 163-166
    • Islam, S.1    Zeisel, A.2    Joost, S.3    Manno, G.4    Zajac, P.5    Kasper, M.6
  • 23
    • 84893905629 scopus 로고    scopus 로고
    • Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
    • Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science. 2014;343:776-9.
    • (2014) Science , vol.343 , pp. 776-779
    • Jaitin, D.A.1    Kenigsberg, E.2    Keren-Shaul, H.3    Elefant, N.4    Paul, F.5    Zaretsky, I.6
  • 25
    • 84864880991 scopus 로고    scopus 로고
    • Full-length mrNA-seq from single-cell levels of rNA and individual circulating tumor cells
    • Ramsköld D, Luo S, Wang Y-C, Li R, Deng Q, Faridani OR, et al. Full-length mrNA-seq from single-cell levels of rNA and individual circulating tumor cells. Nat Biotechnol. 2012;30:777-82.
    • (2012) Nat Biotechnol , vol.30 , pp. 777-782
    • Ramsköld, D.1    Luo, S.2    Wang, Y.-C.3    Li, R.4    Deng, Q.5    Faridani, O.R.6
  • 27
    • 84907500627 scopus 로고    scopus 로고
    • RNA-Seq gene profiling--a systematic empirical comparison
    • Fonseca NA, Marioni J, Brazma A. RNA-Seq gene profiling--a systematic empirical comparison. PLoS One. 2014;9:e107026.
    • (2014) PLoS One , vol.9 , pp. e107026
    • Fonseca, N.A.1    Marioni, J.2    Brazma, A.3
  • 28
    • 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 Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11:R86.
    • (2010) Genome Biol , vol.11 , pp. R86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 30
    • 79959567069 scopus 로고    scopus 로고
    • Deterministic and stochastic allele specific gene expression in single mouse blastomeres
    • Tang F, Barbacioru C, Nordman E, Bao S, Lee C, Wang X, et al. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One. 2011;6:e21208.
    • (2011) PLoS One , vol.6 , pp. e21208
    • Tang, F.1    Barbacioru, C.2    Nordman, E.3    Bao, S.4    Lee, C.5    Wang, X.6
  • 31
    • 84944901262 scopus 로고    scopus 로고
    • Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression
    • Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat Commun. 2015;6:8687.
    • (2015) Nat Commun , vol.6 , pp. 8687
    • Kim, J.K.1    Kolodziejczyk, A.A.2    Ilicic, T.3    Teichmann, S.A.4    Marioni, J.C.5
  • 32
    • 84883364264 scopus 로고    scopus 로고
    • Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
    • Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc. 2013;8:1765-86.
    • (2013) Nat Protoc , vol.8 , pp. 1765-1786
    • Anders, S.1    McCarthy, D.J.2    Chen, Y.3    Okoniewski, M.4    Smyth, G.K.5    Huber, W.6
  • 33
    • 84907267817 scopus 로고    scopus 로고
    • Progressive increase in mtDNA 3243A > G heteroplasmy causes abrupt transcriptional reprogramming
    • Picard M, Zhang J, Hancock S, Derbeneva O, Golhar R, Golik P, et al. Progressive increase in mtDNA 3243A > G heteroplasmy causes abrupt transcriptional reprogramming. Proc Natl Acad Sci U S A. 2014;111:E4033-42.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. E4033-E4042
    • Picard, M.1    Zhang, J.2    Hancock, S.3    Derbeneva, O.4    Golhar, R.5    Golik, P.6
  • 34
    • 84870206960 scopus 로고    scopus 로고
    • Mitochondria: master regulators of danger signalling
    • Galluzzi L, Kepp O, Kroemer G. Mitochondria: master regulators of danger signalling. Nat Rev Mol Cell Biol. 2012;13:780-8.
    • (2012) Nat Rev Mol Cell Biol , vol.13 , pp. 780-788
    • Galluzzi, L.1    Kepp, O.2    Kroemer, G.3
  • 35
    • 35448960851 scopus 로고    scopus 로고
    • Functions and dysfunctions of mitochondrial dynamics
    • Detmer SA, Chan DC. Functions and dysfunctions of mitochondrial dynamics. Nat Rev Mol Cell Biol. 2007;8:870-9.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 870-879
    • Detmer, S.A.1    Chan, D.C.2
  • 36
    • 84895069488 scopus 로고    scopus 로고
    • Quantitative single-cell RNA-seq with unique molecular identifiers
    • Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Meth. 2013;11:163-6.
    • (2013) Nat Meth , vol.11 , pp. 163-166
    • Islam, S.1    Zeisel, A.2    Joost, S.3    Manno, G.4    Zajac, P.5    Kasper, M.6
  • 37
    • 18144430568 scopus 로고    scopus 로고
    • Multivariate outlier detection in exploration geochemistry
    • Filzmoser P, Garrett RG, Reimann C. Multivariate outlier detection in exploration geochemistry. Comput Geosci. 2005;31:579-87.
    • (2005) Comput Geosci , vol.31 , pp. 579-587
    • Filzmoser, P.1    Garrett, R.G.2    Reimann, C.3
  • 38
    • 84155170296 scopus 로고    scopus 로고
    • topGO: topGO: Enrichment analysis for Gene Ontology
    • Alexa A, Rahnenfuhrer J. topGO: topGO: Enrichment analysis for Gene Ontology. 2010.
    • (2010)
    • Alexa, A.1    Rahnenfuhrer, J.2
  • 39
    • 84860351082 scopus 로고    scopus 로고
    • The transcriptional and epigenomic foundations of ground state pluripotency
    • Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell. 2012;149:590-604.
    • (2012) Cell , vol.149 , pp. 590-604
    • Marks, H.1    Kalkan, T.2    Menafra, R.3    Denissov, S.4    Jones, K.5    Hofemeister, H.6
  • 40
    • 84958090257 scopus 로고    scopus 로고
    • Doublet Rate and Detection on the C1 IFCs White Paper
    • (PN 101-2711 A1)
    • Fluidigm Corporation. Doublet Rate and Detection on the C1 IFCs White Paper (PN 101-2711 A1). 2016. p. 1-12.
    • (2016) , pp. 1-12
  • 41
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 42
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012;9:357-9.
    • (2012) Nat Meth , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 43
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 44
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-95.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 45
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010;26:873-81.
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 47
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-11.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 48
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 49
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-a Python framework to work with high-throughput sequencing data
    • btu638-169.
    • Anders S, Pyl PT, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014;31:btu638-169.
    • (2014) Bioinformatics , vol.31
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 50
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511-5.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Baren, M.J.6
  • 51
    • 84877309040 scopus 로고    scopus 로고
    • Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
    • Väremo L, Nielsen J, Nookaew I. Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res. 2013;41:4378-91.
    • (2013) Nucleic Acids Res , vol.41 , pp. 4378-4391
    • Väremo, L.1    Nielsen, J.2    Nookaew, I.3
  • 52
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews BW. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta. 1975;405:442-51.
    • (1975) Biochim Biophys Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 53
    • 84940412877 scopus 로고    scopus 로고
    • Misc Functions of the Department of Statistics, Probability Theory Group
    • (Formerly: E1071), TU Wien
    • Meyer D, Dimitriadou E, Hornik K, Weingessel A, Leisch F. Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. 2015.
    • (2015)
    • Meyer, D.1    Dimitriadou, E.2    Hornik, K.3    Weingessel, A.4    Leisch, F.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.