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Volumn 10, Issue , 2017, Pages 439-462

Single-cell transcriptional analysis

Author keywords

Gene expression; Heterogeneity; Microfluidics; Next generation sequencing; RNA seq

Indexed keywords

BIOINFORMATICS; CELLS; GENE EXPRESSION; MICROFLUIDICS; MOLECULAR BIOLOGY; RNA;

EID: 85020700849     PISSN: 19361327     EISSN: 19361335     Source Type: Book Series    
DOI: 10.1146/annurev-anchem-061516-045228     Document Type: Review
Times cited : (88)

References (98)
  • 2
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro E, Biezuner T, Linnarsson S. (2013). Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 14(9): 618-30
    • (2013) Nat. Rev. Genet , vol.14 , Issue.9 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 3
    • 84894630323 scopus 로고    scopus 로고
    • Entering the era of single-cell transcriptomics in biology and medicine
    • Sandberg R. (2014). Entering the era of single-cell transcriptomics in biology and medicine. Nat. Methods 11(1): 22-24
    • (2014) Nat. Methods , vol.11 , Issue.1 , pp. 22-24
    • Sandberg, R.1
  • 4
    • 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. (2014). Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell 157(1): 8-11
    • (2014) Cell , vol.157 , Issue.1 , pp. 8-11
    • Junker, J.P.1    Van Oudenaarden, A.2
  • 5
    • 84923647450 scopus 로고    scopus 로고
    • Computational and analytical challenges in single-cell transcriptomics
    • Stegle O, Teichmann SA, Marioni JC. (2015). Computational and analytical challenges in single-cell transcriptomics. Nat. Rev. Genet. 16(3): 133-45
    • (2015) Nat. Rev. Genet , vol.16 , Issue.3 , pp. 133-145
    • Stegle, O.1    Teichmann, S.A.2    Marioni, J.C.3
  • 7
    • 84929661801 scopus 로고    scopus 로고
    • Advances and applications of single-cell sequencing technologies
    • Wang Y, Navin NE. (2015). Advances and applications of single-cell sequencing technologies. Mol. Cell 58(4): 598-609
    • (2015) Mol. Cell , vol.58 , Issue.4 , pp. 598-609
    • Wang, Y.1    Navin, N.E.2
  • 8
    • 84959122613 scopus 로고    scopus 로고
    • Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
    • Leng N, Chu L-F, Barry C, Li Y, Choi J, et al. (2015). Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nat. Methods 12(10): 947-50
    • (2015) Nat. Methods , vol.12 , Issue.10 , pp. 947-950
    • Leng, N.1    Chu, L.-F.2    Barry, C.3    Li, Y.4    Choi, J.5
  • 9
    • 84900529199 scopus 로고    scopus 로고
    • Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
    • Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, et al. (2014). Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509(7500): 371-75
    • (2014) Nature , vol.509 , Issue.7500 , pp. 371-375
    • Treutlein, B.1    Brownfield, D.G.2    Wu, A.R.3    Neff, N.F.4    Mantalas, G.L.5
  • 10
    • 84931274624 scopus 로고    scopus 로고
    • A survey of human brain transcriptome diversity at the single cell level
    • Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, et al. (2015). A survey of human brain transcriptome diversity at the single cell level. PNAS 112(23): 7285-90
    • (2015) PNAS , vol.112 , Issue.23 , pp. 7285-7290
    • Darmanis, S.1    Sloan, S.A.2    Zhang, Y.3    Enge, M.4    Caneda, C.5
  • 11
    • 84946226911 scopus 로고    scopus 로고
    • Design and analysis of single-cell sequencing experiments
    • Grün D, van Oudenaarden A. (2015). Design and analysis of single-cell sequencing experiments. Cell 163(4): 799-810
    • (2015) Cell , vol.163 , Issue.4 , pp. 799-810
    • Grün, D.1    Van Oudenaarden, A.2
  • 12
    • 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, et al. (2014). The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32(4): 381-86
    • (2014) Nat. Biotechnol , vol.32 , Issue.4 , pp. 381-386
    • Trapnell, C.1    Cacchiarelli, D.2    Grimsby, J.3    Pokharel, P.4    Li, S.5
  • 13
    • 84975473183 scopus 로고    scopus 로고
    • Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq
    • Treutlein B, Lee QY, Camp JG, Mall M, Koh W, et al. (2016). Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature 534(7607): 391-95
    • (2016) Nature , vol.534 , Issue.7607 , pp. 391-395
    • Treutlein, B.1    Lee, Q.Y.2    Camp, J.G.3    Mall, M.4    Koh, W.5
  • 14
    • 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, et al. (2012). Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol. 30(8): 777-78
    • (2012) Nat. Biotechnol , vol.30 , Issue.8 , pp. 777-778
    • Ramsköld, D.1    Luo, S.2    Wang, Y.-C.3    Li, R.4    Deng, Q.5
  • 15
    • 84942904757 scopus 로고    scopus 로고
    • RNA-seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance
    • Miyamoto DT, Zheng Y, Wittner BS, Lee RJ, Zhu H, et al. (2015). RNA-seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance. Science 349(6254): 1351-56
    • (2015) Science , vol.349 , Issue.6254 , pp. 1351-1356
    • Miyamoto, D.T.1    Zheng, Y.2    Wittner, B.S.3    Lee, R.J.4    Zhu, H.5
  • 16
    • 67349146589 scopus 로고    scopus 로고
    • mRNA-Seq whole-Transcriptome analysis of a single cell
    • Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, et al. (2009). mRNA-Seq whole-Transcriptome analysis of a single cell. Nat. Methods 6(5): 377-82
    • (2009) Nat. Methods , vol.6 , Issue.5 , pp. 377-382
    • Tang, F.1    Barbacioru, C.2    Wang, Y.3    Nordman, E.4    Lee, C.5
  • 17
    • 84894624480 scopus 로고    scopus 로고
    • Dissecting genomic diversity, one cell at a time
    • Blainey PC, Quake SR. (2013). Dissecting genomic diversity, one cell at a time. Nat. Methods 11(1): 19-21
    • (2013) Nat. Methods , vol.11 , Issue.1 , pp. 19-21
    • Blainey, P.C.1    Quake, S.R.2
  • 18
    • 77956412152 scopus 로고    scopus 로고
    • Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis
    • Tang F, Barbacioru C, Bao S, Lee C, Nordman E, et al. (2010). Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6(5): 468-78
    • (2010) Cell Stem Cell , vol.6 , Issue.5 , pp. 468-478
    • Tang, F.1    Barbacioru, C.2    Bao, S.3    Lee, C.4    Nordman, E.5
  • 19
    • 84883743509 scopus 로고    scopus 로고
    • Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
    • Yan L, Yang M, Guo H, Yang L, Wu J, et al. (2013). Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20(9): 1131-39
    • (2013) Nat. Struct. Mol. Biol , vol.20 , Issue.9 , pp. 1131-1139
    • Yan, L.1    Yang, M.2    Guo, H.3    Yang, L.4    Wu, J.5
  • 20
    • 84979663262 scopus 로고    scopus 로고
    • Spatiotemporal reconstruction of the human blastocyst by single-cell gene-expression analysis informs induction of naive pluripotency
    • Durruthy-Durruthy J, Wossidlo M, Pai S, Takahashi Y, Kang G, et al. (2016). Spatiotemporal reconstruction of the human blastocyst by single-cell gene-expression analysis informs induction of naive pluripotency. Dev. Cell 38(1): 100-15
    • (2016) Dev. Cell , vol.38 , Issue.1 , pp. 100-115
    • Durruthy-Durruthy, J.1    Wossidlo, M.2    Pai, S.3    Takahashi, Y.4    Kang, G.5
  • 21
    • 84962688754 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos
    • Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula SP, et al. (2016). Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 165(4): 1012-26
    • (2016) Cell , vol.165 , Issue.4 , pp. 1012-1026
    • Petropoulos, S.1    Edsgärd, D.2    Reinius, B.3    Deng, Q.4    Panula, S.P.5
  • 22
    • 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, et al. (2014). Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510(7505): 363-69
    • (2014) Nature , vol.510 , Issue.7505 , pp. 363-369
    • Shalek, A.K.1    Satija, R.2    Shuga, J.3    Trombetta, J.J.4    Gennert, D.5
  • 23
    • 84956600040 scopus 로고    scopus 로고
    • Olfactory sensory neurons transiently express multiple olfactory receptors during development
    • Tan L, Li Q, Xie XS. (2015). Olfactory sensory neurons transiently express multiple olfactory receptors during development. Mol. Syst. Biol. 11(12): 844-44
    • (2015) Mol. Syst. Biol , vol.11 , Issue.12 , pp. 844-944
    • Tan, L.1    Li, Q.2    Xie, X.S.3
  • 24
    • 84963544829 scopus 로고    scopus 로고
    • Single-cell analysis of long noncoding RNAs in the developing human neocortex
    • Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, et al. (2016). Single-cell analysis of long noncoding RNAs in the developing human neocortex. Genome Biol. 17(1): 67
    • (2016) Genome Biol , vol.17 , Issue.1 , pp. 67
    • Liu, S.J.1    Nowakowski, T.J.2    Pollen, A.A.3    Lui, J.H.4    Horlbeck, M.A.5
  • 25
    • 0025879424 scopus 로고
    • Complementary DNA sequencing: Expressed sequence tags and human genome project
    • Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, et al. (1991). Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252(5013): 1651-56
    • (1991) Science , vol.252 , Issue.5013 , pp. 1651-1656
    • Adams, M.D.1    Kelley, J.M.2    Gocayne, J.D.3    Dubnick, M.4    Polymeropoulos, M.H.5
  • 28
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001). Initial sequencing and analysis of the human genome. Nature 409(6822): 860-921
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2    Birren, B.3    Nusbaum, C.4    Zody, M.C.5
  • 29
    • 0036337915 scopus 로고    scopus 로고
    • A genomic view of alternative splicing
    • Modrek B, Lee C. (2002). A genomic view of alternative splicing. Nat. Genet. 30(1): 13-19
    • (2002) Nat. Genet , vol.30 , Issue.1 , pp. 13-19
    • Modrek, B.1    Lee, C.2
  • 31
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10(1): 57-63
    • (2009) Nat. Rev. Genet , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 32
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9): 1105-11
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 34
    • 84907509527 scopus 로고    scopus 로고
    • Complementary sequence-mediated exon circularization
    • Zhang X-O, Wang H-B, Zhang Y, Lu X, Chen L-L, Yang L. (2014). Complementary sequence-mediated exon circularization. Cell 159(1): 134-47
    • (2014) Cell , vol.159 , Issue.1 , pp. 134-147
    • Zhang, X.-O.1    Wang, H.-B.2    Zhang, Y.3    Lu, X.4    Chen, L.-L.5    Yang, L.6
  • 35
    • 84937703271 scopus 로고    scopus 로고
    • Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    • Fan X, Zhang X, Wu X, Guo H, Hu Y, et al. (2015). Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 16: 148
    • (2015) Genome Biol , vol.16 , pp. 148
    • Fan, X.1    Zhang, X.2    Wu, X.3    Guo, H.4    Hu, Y.5
  • 36
    • 84975453373 scopus 로고    scopus 로고
    • Tracing the expression of circular RNAs in human pre-implantation embryos
    • Dang Y, Yan L, Hu B, Fan X, Ren Y, et al. (2016). Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biol. 17(1): 1-15
    • (2016) Genome Biol , vol.17 , Issue.1 , pp. 1-15
    • Dang, Y.1    Yan, L.2    Hu, B.3    Fan, X.4    Ren, Y.5
  • 37
    • 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, et al. (2014). Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343(6172): 776-79
    • (2014) Science , vol.343 , Issue.6172 , pp. 776-779
    • Jaitin, D.A.1    Kenigsberg, E.2    Keren-Shaul, H.3    Elefant, N.4    Paul, F.5
  • 38
    • 84924565530 scopus 로고    scopus 로고
    • Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
    • Zeisel A, Mũnoz-Manchado AB, Codeluppi S, Lönnerberg P, La Manno G, et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347(6226): 1138-42
    • (2015) Science , vol.347 , Issue.6226 , pp. 1138-1142
    • Zeisel, A.1    Mũnoz-Manchado, A.B.2    Codeluppi, S.3    Lönnerberg, P.4    La Manno, G.5
  • 39
    • 84971222346 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals cell type-specific transcriptional signatures at the maternal-foetal interface during pregnancy
    • Nelson AC, Mould AW, Bikoff EK, Robertson EJ. (2016). Single-cell RNA-seq reveals cell type-specific transcriptional signatures at the maternal-foetal interface during pregnancy. Nat. Commun. 7: 11414
    • (2016) Nat. Commun , vol.7 , pp. 11414
    • Nelson, A.C.1    Mould, A.W.2    Bikoff, E.K.3    Robertson, E.J.4
  • 40
    • 84958078627 scopus 로고    scopus 로고
    • The heterogeneity of humanCD127+ innate lymphoid cells revealed by single-cell RNA sequencing
    • Björklund Å K, Forkel M, Picelli S, Konya V, Theorell J, et al. (2016). The heterogeneity of humanCD127+ innate lymphoid cells revealed by single-cell RNA sequencing. Nat. Immunol. 17(4): 451-60
    • (2016) Nat. Immunol , vol.17 , Issue.4 , pp. 451-460
    • Björklund, Å.K.1    Forkel, M.2    Picelli, S.3    Konya, V.4    Theorell, J.5
  • 41
    • 84902668801 scopus 로고    scopus 로고
    • Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
    • Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, et al. (2014). Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344(6190): 1396-401
    • (2014) Science , vol.344 , Issue.6190 , pp. 1396-1401
    • Patel, A.P.1    Tirosh, I.2    Trombetta, J.J.3    Shalek, A.K.4    Gillespie, S.M.5
  • 42
    • 84969787245 scopus 로고    scopus 로고
    • Tracing haematopoietic stem cell formation at single-cell resolution
    • Zhou F, Li X, Wang W, Zhu P, Zhou J, et al. (2016). Tracing haematopoietic stem cell formation at single-cell resolution. Nature 533(7604): 487-92
    • (2016) Nature , vol.533 , Issue.7604 , pp. 487-492
    • Zhou, F.1    Li, X.2    Wang, W.3    Zhu, P.4    Zhou, J.5
  • 43
    • 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, et al. (2015). Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161(5): 1202-14
    • (2015) Cell , vol.161 , Issue.5 , pp. 1202-1214
    • Macosko, E.Z.1    Basu, A.2    Satija, R.3    Nemesh, J.4    Shekhar, K.5
  • 44
    • 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, et al. (2015). Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161(5): 1187-201
    • (2015) Cell , vol.161 , Issue.5 , pp. 1187-1201
    • Klein, A.M.1    Mazutis, L.2    Akartuna, I.3    Tallapragada, N.4    Veres, A.5
  • 45
  • 46
    • 84988884535 scopus 로고    scopus 로고
    • An automated microwell platform for large-scale single cell RNA-Seq
    • Yuan J, Sims PA. (2016). An automated microwell platform for large-scale single cell RNA-Seq. Sci. Rep. 6: 33883
    • (2016) Sci. Rep , vol.6 , pp. 33883
    • Yuan, J.1    Sims, P.A.2
  • 47
    • 84897528076 scopus 로고    scopus 로고
    • Cartography of neurexin alternative splicingmapped by single-molecule long-read mRNA sequencing
    • Treutlein B, Gokce O, Quake SR, Südhof TC. (2014). Cartography of neurexin alternative splicingmapped by single-molecule long-read mRNA sequencing. PNAS 111(13): E1291-99
    • (2014) PNAS , vol.111 , Issue.13 , pp. E1291-E1299
    • Treutlein, B.1    Gokce, O.2    Quake, S.R.3    Südhof, T.C.4
  • 48
    • 84958103478 scopus 로고    scopus 로고
    • Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells
    • Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F, et al. (2016). Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells. Cell Rep. 14(4): 966-77
    • (2016) Cell Rep , vol.14 , Issue.4 , pp. 966-977
    • Macaulay, I.C.1    Svensson, V.2    Labalette, C.3    Ferreira, L.4    Hamey, F.5
  • 49
    • 84922334171 scopus 로고    scopus 로고
    • How deep is enough in single-cell RNA-seq?
    • Streets AM, Huang Y. (2014). How deep is enough in single-cell RNA-seq?. Nat. Biotechnol. 32(10): 1005-6
    • (2014) Nat Biotechnol , vol.32 , Issue.10 , pp. 1005-1006
    • Streets, A.M.1    Huang, Y.2
  • 50
    • 84962050673 scopus 로고    scopus 로고
    • Distinct myeloid progenitordifferentiation pathways identified through single-cell RNA sequencing
    • Drissen R, Buza-Vidas N, Woll P, Thongjuea S, Gambardella A, et al. (2016). Distinct myeloid progenitordifferentiation pathways identified through single-cell RNA sequencing. Nat. Immunol. 17(6): 666-76
    • (2016) Nat. Immunol , vol.17 , Issue.6 , pp. 666-676
    • Drissen, R.1    Buza-Vidas, N.2    Woll, P.3    Thongjuea, S.4    Gambardella, A.5
  • 51
    • 84893242996 scopus 로고    scopus 로고
    • RNA-seq differential expression studies: More sequence or more replication?
    • Liu Y, Zhou J, White KP. (2014). RNA-seq differential expression studies: more sequence or more replication?. Bioinformatics 30(3): 301-4
    • (2014) Bioinformatics , vol.30 , Issue.3 , pp. 301-304
    • Liu, Y.1    Zhou, J.2    White, K.P.3
  • 52
    • 84892728434 scopus 로고    scopus 로고
    • Sequencing depth and coverage: Key considerations in genomic analyses
    • Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. (2014). Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet. 15(2): 121-32
    • (2014) Nat. Rev. Genet , vol.15 , Issue.2 , pp. 121-132
    • Sims, D.1    Sudbery, I.2    Ilott, N.E.3    Heger, A.4    Ponting, C.P.5
  • 53
    • 84901831004 scopus 로고    scopus 로고
    • Validation of noise models for single-cell transcriptomics
    • Grün D, Kester L, van Oudenaarden A. (2014). Validation of noise models for single-cell transcriptomics. Nat. Methods 11(6): 637-40
    • (2014) Nat. Methods , vol.11 , Issue.6 , pp. 637-640
    • Grün, D.1    Kester, L.2    Van Oudenaarden, A.3
  • 54
    • 84923358731 scopus 로고    scopus 로고
    • Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
    • Munro SA, Lund SP, Pine PS, Binder H, Clevert D-A, et al. (2014). Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nat. Commun. 5: 5125
    • (2014) Nat. Commun , vol.5 , pp. 5125
    • Munro, S.A.1    Lund, S.P.2    Pine, P.S.3    Binder, H.4    Clevert, D.-A.5
  • 55
  • 56
    • 80052521697 scopus 로고    scopus 로고
    • Synthetic spike-in standards for RNA-seq experiments
    • Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, et al. (2011). Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21(9): 1543-51
    • (2011) Genome Res , vol.21 , Issue.9 , pp. 1543-1551
    • Jiang, L.1    Schlesinger, F.2    Davis, C.A.3    Zhang, Y.4    Li, R.5
  • 57
    • 84970949920 scopus 로고    scopus 로고
    • Howmany biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
    • Schurch NJ, Schofield P, Gierlínski M, Cole C, Sherstnev A, et al. 2016.Howmany biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?. RNA 22(6): 839-51
    • (2016) RNA , vol.22 , Issue.6 , pp. 839-851
    • Schurch, N.J.1    Schofield, P.2    Gierlínski, M.3    Cole, C.4    Sherstnev, A.5
  • 58
    • 84942292053 scopus 로고    scopus 로고
    • How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets
    • Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, et al. (2015). How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets. Nucleic Acids Res. 43(16): 7664-74
    • (2015) Nucleic Acids Res , vol.43 , Issue.16 , pp. 7664-7674
    • Peixoto, L.1    Risso, D.2    Poplawski, S.G.3    Wimmer, M.E.4    Speed, T.P.5
  • 59
    • 0023066863 scopus 로고
    • Second-strand cDNAsyn thesis mRNAfragments as primers
    • Gubler U. (1987). Second-strand cDNAsynthesis: mRNAfragments as primers. Methods Enzymol. 152: 330-35
    • (1987) Methods Enzymol , vol.152 , pp. 330-335
    • Gubler, U.1
  • 60
    • 84876085773 scopus 로고    scopus 로고
    • Quartz-Seq: A highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
    • Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, et al. (2013). Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol. 14(4): R31
    • (2013) Genome Biol , vol.14 , Issue.4 , pp. R31
    • Sasagawa, Y.1    Nikaido, I.2    Hayashi, T.3    Danno, H.4    Uno, K.D.5
  • 61
    • 79959403670 scopus 로고    scopus 로고
    • Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
    • Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, et al. (2011). Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21(7): 1160-67
    • (2011) Genome Res , vol.21 , Issue.7 , pp. 1160-1167
    • Islam, S.1    Kjällquist, U.2    Moliner, A.3    Zajac, P.4    Fan, J.B.5
  • 63
    • 84856398949 scopus 로고    scopus 로고
    • Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
    • Shiroguchi K, Jia TZ, Sims PA, Xie XS. (2012). Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. PNAS 109(4): 1347-52
    • (2012) PNAS , vol.109 , Issue.4 , pp. 1347-1352
    • Shiroguchi, K.1    Jia, T.Z.2    Sims, P.A.3    Xie, X.S.4
  • 64
    • 84866953427 scopus 로고    scopus 로고
    • CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification
    • Hashimshony T, Wagner F, Sher N, Yanai I. (2012). CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2(3): 666-73
    • (2012) Cell Rep , vol.2 , Issue.3 , pp. 666-673
    • Hashimshony, T.1    Wagner, F.2    Sher, N.3    Yanai, I.4
  • 66
    • 84872194966 scopus 로고    scopus 로고
    • Two methods for full-length RNA sequencing for low quantities of cells and single cells
    • Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, et al. (2012). Two methods for full-length RNA sequencing for low quantities of cells and single cells. PNAS 110(2): 594-99
    • (2012) PNAS , vol.110 , Issue.2 , pp. 594-599
    • Pan, X.1    Durrett, R.E.2    Zhu, H.3    Tanaka, Y.4    Li, Y.5
  • 67
    • 84942874388 scopus 로고    scopus 로고
    • Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification
    • Fu Y, Li C, Lu S, Zhou W, Tang F, et al. (2015). Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. PNAS 112(38): 11923-28
    • (2015) PNAS , vol.112 , Issue.38 , pp. 11923-11928
    • Fu, Y.1    Li, C.2    Lu, S.3    Zhou, W.4    Tang, F.5
  • 68
    • 85020717353 scopus 로고    scopus 로고
    • Single cell total RNA sequencing through isothermal amplification in picoliter-droplet emulsion
    • Fu Y, Chen H, Liu L, Huang Y. (2016). Single cell total RNA sequencing through isothermal amplification in picoliter-droplet emulsion. Anal. Chem. 88(22): 10795-99
    • (2016) Anal. Chem , vol.88 , Issue.22 , pp. 10795-10799
    • Fu, Y.1    Chen, H.2    Liu, L.3    Huang, Y.4
  • 69
    • 84913593681 scopus 로고    scopus 로고
    • Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
    • Picelli S, Björklund Å K, Reinius B, Sagasser S, Winberg G, Sandberg R. (2014). Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24(12): 2033-40
    • (2014) Genome Res , vol.24 , Issue.12 , pp. 2033-2040
    • Picelli, S.1    Björklund, Å.K.2    Reinius, B.3    Sagasser, S.4    Winberg, G.5    Sandberg, R.6
  • 70
    • 79953288433 scopus 로고    scopus 로고
    • Development and applications of single-cell transcriptome analysis
    • Tang F, Lao K, Surani MA. (2011). Development and applications of single-cell transcriptome analysis. Nat. Methods 8(4): S6-11
    • (2011) Nat. Methods , vol.8 , Issue.4 , pp. S6-S11
    • Tang, F.1    Lao, K.2    Surani, M.A.3
  • 71
    • 84893910301 scopus 로고    scopus 로고
    • Quantitative assessment of single-cell RNA-sequencing methods
    • Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, et al. (2014). Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods 11(1): 41-46
    • (2014) Nat. Methods , vol.11 , Issue.1 , pp. 41-46
    • Wu, A.R.1    Neff, N.F.2    Kalisky, T.3    Dalerba, P.4    Treutlein, B.5
  • 72
    • 84922311090 scopus 로고    scopus 로고
    • Combinatorial labeling of single cells for gene expression cytometry
    • Fan HC, Fu GK, Fodor SPA. (2015). Combinatorial labeling of single cells for gene expression cytometry. Science 347(6222): 1258367
    • (2015) Science , vol.347 , Issue.6222 , pp. 1258367
    • Fan, H.C.1    Fu, G.K.2    Fodor, S.P.A.3
  • 74
    • 84900517167 scopus 로고    scopus 로고
    • Microfluidic single-cell whole-Transcriptome sequencing
    • Streets AM, Zhang X, Cao C, Pang Y, Wu X, et al. (2014). Microfluidic single-cell whole-Transcriptome sequencing. PNAS 111(19): 7048-53
    • (2014) PNAS , vol.111 , Issue.19 , pp. 7048-7053
    • Streets, A.M.1    Zhang, X.2    Cao, C.3    Pang, Y.4    Wu, X.5
  • 75
    • 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, et al. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28(5): 511-15
    • (2010) Nat. Biotechnol , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5
  • 76
    • 84872033704 scopus 로고    scopus 로고
    • Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
    • Wagner GP, Kin K, Lynch VJ. (2012). Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 131(4): 281-85
    • (2012) Theory Biosci , vol.131 , Issue.4 , pp. 281-285
    • Wagner, G.P.1    Kin, K.2    Lynch, V.J.3
  • 77
    • 84893473154 scopus 로고    scopus 로고
    • Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations
    • Fu GK, Xu W, Wilhelmy J, Mindrinos MN, Davis RW, et al. (2014). Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations. PNAS 111(5): 1891-96
    • (2014) PNAS , vol.111 , Issue.5 , pp. 1891-1896
    • Fu, G.K.1    Xu, W.2    Wilhelmy, J.3    Mindrinos, M.N.4    Davis, R.W.5
  • 78
    • 84895069488 scopus 로고    scopus 로고
    • Quantitative single-cell RNA-seq with unique molecular identifiers
    • Islam S, Zeisel A, Joost S, LaManno G, Zajac P, et al. (2013). Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods 11: 163-66
    • (2013) Nat. Methods , vol.11 , pp. 163-166
    • Islam, S.1    Zeisel, A.2    Joost, S.3    LaManno, G.4    Zajac, P.5
  • 80
    • 85008384488 scopus 로고    scopus 로고
    • Batch effects and the effective design of single-cell gene expression studies
    • Tung P-Y, Blischak JD, Hsiao C, Knowles DA, Burnett JE, et al. (2017). Batch effects and the effective design of single-cell gene expression studies. Sci. Rep. 8: 39921
    • (2017) Sci. Rep , vol.8 , pp. 39921
    • Tung, P.-Y.1    Blischak, J.D.2    Hsiao, C.3    Knowles, D.A.4    Burnett, J.E.5
  • 81
    • 84909644283 scopus 로고    scopus 로고
    • Normalization of RNA-seq data using factor analysis of control genes or samples
    • Risso D, Ngai J, Speed TP, Dudoit S. (2014). Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32(9): 896-902
    • (2014) Nat. Biotechnol , vol.32 , Issue.9 , pp. 896-902
    • Risso, D.1    Ngai, J.2    Speed, T.P.3    Dudoit, S.4
  • 82
    • 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, et al. (2015). Computational analysis of cell-To-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 33(2): 155-60
    • (2015) Nat. Biotechnol , vol.33 , Issue.2 , pp. 155-160
    • Buettner, F.1    Natarajan, K.N.2    Casale, F.P.3    Proserpio, V.4    Scialdone, A.5
  • 83
    • 84953226880 scopus 로고    scopus 로고
    • BASiCS: Bayesian analysis of single-cell sequencing data
    • Vallejos CA, Marioni JC, Richardson S. (2015). BASiCS: Bayesian analysis of single-cell sequencing data. PLOS Comput. Biol. 11(6): e1004333
    • (2015) PLOS Comput. Biol , vol.11 , Issue.6 , pp. e1004333
    • Vallejos, C.A.1    Marioni, J.C.2    Richardson, S.3
  • 84
    • 84964556059 scopus 로고    scopus 로고
    • Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
    • Lun ATL, Bach K, Marioni JC. (2016). Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17(1): 75
    • (2016) Genome Biol , vol.17 , Issue.1 , pp. 75
    • Lun, A.T.L.1    Bach, K.2    Marioni, J.C.3
  • 85
    • 84887109584 scopus 로고    scopus 로고
    • Accounting for technical noise in single-cell RNA-seq experiments
    • Brennecke P, Anders S, Kim JK, Kolodziejczyk AA, Zhang X, et al. (2013). Accounting for technical noise in single-cell RNA-seq experiments. Nat. Methods 10(11): 1093-95
    • (2013) Nat. Methods , vol.10 , Issue.11 , pp. 1093-1095
    • Brennecke, P.1    Anders, S.2    Kim, J.K.3    Kolodziejczyk, A.A.4    Zhang, X.5
  • 86
    • 84959189722 scopus 로고    scopus 로고
    • Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis
    • Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, et al. (2016). Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat. Methods 13(3): 241-44
    • (2016) Nat. Methods , vol.13 , Issue.3 , pp. 241-244
    • Fan, J.1    Salathia, N.2    Liu, R.3    Kaeser, G.E.4    Yung, Y.C.5
  • 87
    • 84892179132 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic random monoallelic gene expression in mammalian cells
    • Deng Q, Ramsköld D, Reinius B, Sandberg R. (2014). Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343(6167): 193-96
    • (2014) Science , vol.343 , Issue.6167 , pp. 193-196
    • Deng, Q.1    Ramsköld, D.2    Reinius, B.3    Sandberg, R.4
  • 88
    • 84949293695 scopus 로고    scopus 로고
    • SINCERA: A pipeline for single-cell RNA-Seq profiling analysis
    • Guo M, Wang H, Potter SS, Whitsett JA, Xu Y. (2015). SINCERA: a pipeline for single-cell RNA-Seq profiling analysis. PLOS Comput. Biol. 11(11): e1004575
    • (2015) PLOS Comput. Biol , vol.11 , Issue.11 , pp. e1004575
    • Guo, M.1    Wang, H.2    Potter, S.S.3    Whitsett, J.A.4    Xu, Y.5
  • 89
    • 84947805126 scopus 로고    scopus 로고
    • Sincell: An R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq
    • Juliá M, Telenti A, Rausell A. (2015). Sincell: An R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq. Bioinformatics 31(20): 3380-82
    • (2015) Bioinformatics , vol.31 , Issue.20 , pp. 3380-3382
    • Juliá, M.1    Telenti, A.2    Rausell, A.3
  • 90
    • 84941010341 scopus 로고    scopus 로고
    • Single-cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis
    • Shin J, Berg DA, Zhu Y, Shin JY, Song J, et al. (2015). Single-cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis. Cell 17(3): 360-72
    • (2015) Cell , vol.17 , Issue.3 , pp. 360-372
    • Shin, J.1    Berg, D.A.2    Zhu, Y.3    Shin, J.Y.4    Song, J.5
  • 91
    • 84977499231 scopus 로고    scopus 로고
    • PcaReduce: Hierarchical clustering of single cell transcriptional profiles
    • Žurauskiene J, Yau C. (2016). pcaReduce: hierarchical clustering of single cell transcriptional profiles. BMC Bioinform. 17(1): 140
    • (2016) BMC Bioinform , vol.17 , Issue.1 , pp. 140
    • Žurauskiene, J.1    Yau, C.2
  • 92
    • 84974587998 scopus 로고    scopus 로고
    • Wishbone identifies bifurcating developmental trajectories from single-cell data
    • Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, et al. (2016). Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat. Biotechnol. 34(6): 637-45
    • (2016) Nat. Biotechnol , vol.34 , Issue.6 , pp. 637-645
    • Setty, M.1    Tadmor, M.D.2    Reich-Zeliger, S.3    Angel, O.4    Salame, T.M.5
  • 93
    • 84955706109 scopus 로고    scopus 로고
    • ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis
    • Pierson E, Yau C. (2015). ZIFA: dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol. 16(1): 241
    • (2015) Genome Biol , vol.16 , Issue.1 , pp. 241
    • Pierson, E.1    Yau, C.2
  • 95
    • 84880280631 scopus 로고    scopus 로고
    • ViSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia
    • Amir ED, Davis KL, Tadmor MD, Simonds EF, Levine JH, et al. (2013). ViSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat. Biotechnol. 31(6): 545-52
    • (2013) Nat. Biotechnol , vol.31 , Issue.6 , pp. 545-552
    • Amir, E.D.1    Davis, K.L.2    Tadmor, M.D.3    Simonds, E.F.4    Levine, J.H.5
  • 96
    • 84941201582 scopus 로고    scopus 로고
    • Single-cell messenger RNA sequencing reveals rare intestinal cell types
    • Grün D, Lyubimova A, Kester L, Wiebrands K, Basak O, et al. (2015). Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525(7568): 251-55
    • (2015) Nature , vol.525 , Issue.7568 , pp. 251-255
    • Grün, D.1    Lyubimova, A.2    Kester, L.3    Wiebrands, K.4    Basak, O.5
  • 97
    • 84899574465 scopus 로고    scopus 로고
    • Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development
    • Bendall SC, Davis KL, Amir ED, Tadmor MD, Simonds EF, et al. (2014). Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157(3): 714-25
    • (2014) Cell , vol.157 , Issue.3 , pp. 714-725
    • Bendall, S.C.1    Davis, K.L.2    Amir, E.D.3    Tadmor, M.D.4    Simonds, E.F.5
  • 98
    • 84924365758 scopus 로고    scopus 로고
    • Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
    • Marco E, Karp RL, Guo G, Robson P, Hart AH, et al. (2014). Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. PNAS 111(52): E5643-50
    • (2014) PNAS , vol.111 , Issue.52 , pp. E5643-E5650
    • Marco, E.1    Karp, R.L.2    Guo, G.3    Robson, P.4    Hart, A.H.5


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