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Volumn 17, Issue 4, 2018, Pages 233-239

Experimental design for single-cell RNA sequencing

Author keywords

10x Chromium; Drop Seq; Experimental design; Single cell RNA sequencing; Smart Seq 2

Indexed keywords

ARTICLE; EXPERIMENTAL DESIGN; HUMAN CELL; RNA SEQUENCE; GENE EXPRESSION PROFILING; MICROFLUIDIC ANALYSIS; PROCEDURES; SEQUENCE ANALYSIS; SINGLE CELL ANALYSIS;

EID: 85043529587     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elx035     Document Type: Article
Times cited : (100)

References (29)
  • 1
    • 84962229210 scopus 로고    scopus 로고
    • Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells
    • Grover A, Sanjuan-Pla A, Thongjuea S, et al. Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells. Nat Commun 2016;7:11075.
    • (2016) Nat Commun , vol.7 , pp. 11075
    • Grover, A.1    Sanjuan-Pla, A.2    Thongjuea, S.3
  • 2
    • 85019709160 scopus 로고    scopus 로고
    • Proliferation drives aging-related functional decline in a subpopulation of the hem-atopoietic stem cell compartment
    • Kirschner K, Chandra T, Kiselev V, et al. Proliferation drives aging-related functional decline in a subpopulation of the hem-atopoietic stem cell compartment. Cell Rep 2017;19(8):1503-11.
    • (2017) Cell Rep , vol.19 , Issue.8 , pp. 1503-1511
    • Kirschner, K.1    Chandra, T.2    Kiselev, V.3
  • 3
    • 84922321862 scopus 로고    scopus 로고
    • Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
    • Pollen AA, Nowakowski TJ, Shuga J, et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotech 2014;32(10):1053-8.
    • (2014) Nat Biotech , vol.32 , Issue.10 , pp. 1053-1058
    • Pollen, A.A.1    Nowakowski, T.J.2    Shuga, J.3
  • 4
    • 85016148799 scopus 로고    scopus 로고
    • Single-cell spatial reconstruction reveals global division of labour in the mammalian liver
    • Halpern KB, Shenhav R, Matcovitch-Natan O, et al. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature 2017;542(7641):352-6.
    • (2017) Nature , vol.542 , Issue.7641 , pp. 352-356
    • Halpern, K.B.1    Shenhav, R.2    Matcovitch-Natan, O.3
  • 5
    • 84891677425 scopus 로고    scopus 로고
    • Full-length RNA-seq from single cells using Smart-seq2
    • Picelli S, Faridani OR, Björklund ÅK, et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 2014;9(1):171-81.
    • (2014) Nat Protoc , vol.9 , Issue.1 , pp. 171-181
    • Picelli, S.1    Faridani, O.R.2    Björklund, A.K.3
  • 6
    • 85028303209 scopus 로고    scopus 로고
    • Comprehensive single-cell transcriptional profiling of a multicellular organism
    • Cao J, Packer JS, Ramani V, et al. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 2017;357(6352):661-7.
    • (2017) Science , vol.357 , Issue.6352 , pp. 661-667
    • Cao, J.1    Packer, J.S.2    Ramani, V.3
  • 7
    • 84929684998 scopus 로고    scopus 로고
    • Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
    • Klein AM, Mazutis L, Akartuna I, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 2015;161(5):1187-201.
    • (2015) Cell , vol.161 , Issue.5 , pp. 1187-1201
    • Klein, A.M.1    Mazutis, L.2    Akartuna, I.3
  • 8
    • 84929684999 scopus 로고    scopus 로고
    • Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
    • Macosko EZ, Basu A, Satija R, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 2015;161(5):1202-14.
    • (2015) Cell , vol.161 , Issue.5 , pp. 1202-1214
    • Macosko, E.Z.1    Basu, A.2    Satija, R.3
  • 9
    • 85019374719 scopus 로고    scopus 로고
    • Cell fixation and preservation for droplet-based single-cell transcriptomics
    • Alles J, Karaiskos N, Praktiknjo SD, et al. Cell fixation and preservation for droplet-based single-cell transcriptomics. BMC Biol 2017;15(1):44.
    • (2017) BMC Biol , vol.15 , Issue.1 , pp. 44
    • Alles, J.1    Karaiskos, N.2    Praktiknjo, S.D.3
  • 10
    • 85018582872 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
    • Villani AC, Satija R, Reynolds G, et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 2017;356(6335).
    • (2017) Science , vol.356 , Issue.6335
    • Villani, A.C.1    Satija, R.2    Reynolds, G.3
  • 11
    • 84962658087 scopus 로고    scopus 로고
    • Design and computational analysis of single-cell RNA-sequencing experiments
    • Bacher R, Kendziorski C. Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biol 2016; 17(1):63.
    • (2016) Genome Biol , vol.17 , Issue.1 , pp. 63
    • Bacher, R.1    Kendziorski, C.2
  • 12
    • 84923647450 scopus 로고    scopus 로고
    • Computational and analytical challenges in single-cell transcriptomics
    • Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet 2015;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
  • 13
    • 85055666799 scopus 로고    scopus 로고
    • Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data
    • Lun ATL, Calero-Nieto FJ, Haim-Vilmovsky L, et al. Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data. bioRxiv 2017.
    • (2017) bioRxiv
    • Lun, A.T.L.1    Calero-Nieto, F.J.2    Haim-Vilmovsky, L.3
  • 14
    • 84895069488 scopus 로고    scopus 로고
    • Quantitative single-cell RNA-seq with unique molecular identifiers
    • Islam S, Zeisel A, Joost S, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods 2014;11(2):163-6.
    • (2014) Nat Methods , vol.11 , Issue.2 , pp. 163-166
    • Islam, S.1    Zeisel, A.2    Joost, S.3
  • 15
    • 85008384488 scopus 로고    scopus 로고
    • Batch effects and the effective design of single-cell gene expression studies
    • Tung PY, Blischak JD, Hsiao CJ, et al. Batch effects and the effective design of single-cell gene expression studies. Sci Rep 2017;7:39921.
    • (2017) Sci Rep , vol.7 , pp. 39921
    • Tung, P.Y.1    Blischak, J.D.2    Hsiao, C.J.3
  • 16
    • 77955504378 scopus 로고    scopus 로고
    • Statistical design and analysis of RNA-seq data
    • Auer PL, Doerge RW. Statistical design and analysis of RNA-seq data. Genetics 2010;185(2):405-16.
    • (2010) Genetics , vol.185 , Issue.2 , pp. 405-416
    • Auer, P.L.1    Doerge, R.W.2
  • 17
    • 0036900895 scopus 로고    scopus 로고
    • Fundamentals of experimental design for cDNA microarrays
    • Churchill GA. Fundamentals of experimental design for cDNA microarrays. Nat Genet 2002;32:490-5.
    • (2002) Nat Genet , vol.32 , pp. 490-495
    • Churchill, G.A.1
  • 18
    • 0000884487 scopus 로고    scopus 로고
    • Experimental design for gene expression microarrays
    • Kerr MK, Churchill GA. Experimental design for gene expression microarrays. Biostatistics 2001;2(2):183-201.
    • (2001) Biostatistics , vol.2 , Issue.2 , pp. 183-201
    • Kerr, M.K.1    Churchill, G.A.2
  • 19
    • 84961169621 scopus 로고    scopus 로고
    • On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-Seq data
    • Hicks SC, Teng M, Irizarry RA. On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-Seq data. bioRxiv 2015.
    • (2015) bioRxiv
    • Hicks, S.C.1    Teng, M.2    Irizarry, R.A.3
  • 20
    • 0034730124 scopus 로고    scopus 로고
    • Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
    • Lee ML, Kuo FC, Whitmore GA, et al. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 2000;97(18):9834-9.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.18 , pp. 9834-9839
    • Lee, M.L.1    Kuo, F.C.2    Whitmore, G.A.3
  • 21
    • 77956873627 scopus 로고    scopus 로고
    • Tackling the widespread and critical impact of batch effects in high-throughput data
    • Leek JT, Scharpf RB, Bravo HC, et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet 2010;11(10):733-9.
    • (2010) Nat Rev Genet , vol.11 , Issue.10 , pp. 733-739
    • Leek, J.T.1    Scharpf, R.B.2    Bravo, H.C.3
  • 22
    • 2542565666 scopus 로고    scopus 로고
    • Gene expression in the urinary bladder: A common carcinoma in situ gene expression signature exists disregarding histopathological classification
    • Dyrskjøt L, Kruhøffer M, Thykjaer T, et al. Gene expression in the urinary bladder: a common carcinoma in situ gene expression signature exists disregarding histopathological classification. Cancer Res 2004;64(11):4040-8.
    • (2004) Cancer Res , vol.64 , Issue.11 , pp. 4040-4048
    • Dyrskjøt, L.1    Kruhøffer, M.2    Thykjaer, T.3
  • 23
    • 84923188586 scopus 로고    scopus 로고
    • Deconstructing transcriptional heterogeneity in pluripotent stem cells
    • Kumar RM, Cahan P, Shalek AK, et al. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 2014;516(7529):56-61.
    • (2014) Nature , vol.516 , Issue.7529 , pp. 56-61
    • Kumar, R.M.1    Cahan, P.2    Shalek, A.K.3
  • 24
    • 84914125316 scopus 로고    scopus 로고
    • Comparison of the transcriptional landscapes between human and mouse tissues
    • Lin S, Lin Y, Nery JR, et al. Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci USA 2014;111(48):17224-9.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.48 , pp. 17224-17229
    • Lin, S.1    Lin, Y.2    Nery, J.R.3
  • 25
    • 84902668801 scopus 로고    scopus 로고
    • Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblast-oma
    • Patel AP, Tirosh I, Trombetta JJ, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblast-oma. Science 2014;344(6190):1396-401.
    • (2014) Science , vol.344 , Issue.6190 , pp. 1396-1401
    • Patel, A.P.1    Tirosh, I.2    Trombetta, J.J.3
  • 26
    • 84940969958 scopus 로고    scopus 로고
    • A reanalysis of mouse ENCODE comparative gene expression data
    • Gilad Y, Mizrahi-Man O. A reanalysis of mouse ENCODE comparative gene expression data. F1000Res 2015;4:121.
    • (2015) F1000Res , vol.4 , pp. 121
    • Gilad, Y.1    Mizrahi-Man, O.2
  • 27
    • 35748952199 scopus 로고    scopus 로고
    • A gene expression barcode for microarray data
    • Zilliox MJ, Irizarry RA. A gene expression barcode for microarray data. Nat Methods 2007;4(11):911-13.
    • (2007) Nat Methods , vol.4 , Issue.11 , pp. 911-913
    • Zilliox, M.J.1    Irizarry, R.A.2
  • 28
    • 85055619307 scopus 로고    scopus 로고
    • Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours
    • Haghverdi L, Lun ATL, Morgan MD, et al. Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours. bioRxiv 2017.
    • (2017) bioRxiv
    • Haghverdi, L.1    Lun, A.T.L.2    Morgan, M.D.3
  • 29
    • 85014524493 scopus 로고    scopus 로고
    • Power analysis of single-cell RNA-sequencing experiments
    • Svensson V, Natarajan KN, Ly LH, et al. Power analysis of single-cell RNA-sequencing experiments. Nat Meth 2017;14(4):381-7.
    • (2017) Nat Meth , vol.14 , Issue.4 , pp. 381-387
    • Svensson, V.1    Natarajan, K.N.2    Ly, L.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.