Defining cell types and states with single-cell genomics

Genome Research

Volumn 25, Issue 10, 2015, Pages 1491-1498

  Trapnell, Cole ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; TRANSCRIPTOME;

ALGORITHM; BLEACHING; CELL DIFFERENTIATION; CELL FATE; CELL INTERACTION; CELLS BY BODY ANATOMY; CELLULAR DISTRIBUTION; CHROMATIN IMMUNOPRECIPITATION; CYTOMETRY; DNA BINDING; DNA SEQUENCE; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENOMICS; HISTONE MODIFICATION; HUMAN; NEXT GENERATION SEQUENCING; NUCLEOSOME; PRIORITY JOURNAL; PROTEOMICS; REVIEW; RNA SEQUENCE; SINGLE CELL ANALYSIS; SINGLE CELL GENOMICS; ANIMAL; CELLS; CYTOLOGY;

ANIMALS; CELLS; CYTOLOGICAL TECHNIQUES; GENOMICS; HUMANS;

EID: 84942940566     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.190595.115     Document Type: Review

References (73)

1. Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, Marioni JC. 2015. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat Biotechnol 33: 503-509.
2. Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D. 2014. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157: 714-725.
3. Beyer K, Goldstein J, Ramakrishnan R, Shaft U. 1999. When is "nearest neighbor" meaningful? In Database theory-ICDT'99 (ed. Beeri C, Buneman P), Vol. 1540 of Lecture Notes in Computer Science, pp. 217-235. Springer, Berlin, Heidelberg, Germany.
4. Boareto M, Jolly MK, Lu M, Onuchic JN, Clementi C, Ben-Jacob E. 2015. Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype. Proc Natl Acad Sci 112: E402-E409.
5. Brennecke P, Anders S, Kim JK, Kolodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, et al. 2013. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods 10: 1093-1095.
6. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 1213-1218.
7. Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. 2015. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523: 486-490.
8. Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. 2015. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol 33: 155-160.
9. Buganim Y, Faddah DA, Cheng AW, Itskovich E, Markoulaki S, Ganz K, Klemm SL, van Oudenaarden A, Jaenisch R. 2012. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150: 1209-1222.
10. Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X. 2015. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348: aaa6090.
11. Cloonan N, Forrest ARR, Kolle G, Gardiner BBA, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619.
12. Collier JR, Monk NA, Maini PK, Lewis JH. 1996. Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling. J Theor Biol 183: 429-446.
13. Crawford GE, David S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. 2006. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods 3: 503-509.
14. Cusanovich DA, Daza R, Adey A, Pliner HA. 2015. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348: 910-914.
15. Dey SS, Spanjaard B, Bienko M, van Oudenaarden A. 2015. Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol 33: 285-289.
16. Durruthy-Durruthy R, Gottlieb A, Hartman BH, Waldhaus J, Laske RD, Altman R, Heller S. 2014. Reconstruction of the mouse otocyst and early neuroblast lineage at single-cell resolution. Cell 157: 964-978.
17. Fan HC, Fu GK, Fodor SP. 2015. Expression profiling. Combinatorial labeling of single cells for gene expression cytometry. Science 347: 1258367.
18. Ferrell JE Jr, Machleder EM. 1998. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280: 895-898.
19. Fu GK, Xu W, Wilhelmy J, Mindrinos MN, Davis RW, Xiao W, Fodor SP. 2014. Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations. Proc Natl Acad Sci 111: 1891-1896.
20. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. 2007. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17: 877-885.
21. Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, O'Shaughnessy AL, Lambert GM, Araúzo-Bravo MJ, Lee J, Fishman M, Robbins GE, et al. 2013. RNA-sequencing from single nuclei. Proc Natl Acad Sci 110: 19802-19807.
22. Grün D, Kester L, van Oudenaarden A. 2014. Validation of noise models for single-cell transcriptomics. Nat Methods 11: 637-640.
23. Guo H, Zhu P,WuX, Li X, WenL, Tang F. 2013. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res 23: 2126-2135.
24. Hashimshony T, Wagner F, Sher N, Yanai I. 2012. CEL-Seq: single-cell RNAseq by multiplexed linear amplification. Cell Rep 2: 666-673.
25. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, et al. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6: 283-289.
26. Huang S, Guo YP, May G, Enver T. 2007. Bifurcation dynamics in lineagecommitment in bipotent progenitor cells. Dev Biol 305: 695-713.
27. Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S. 2011. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21: 1160-1167.
28. Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, Cohen N, Jung S, Tanay A, et al. 2014. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343: 776-779.
29. Johnson DS, Mortazavi A, Myers RM, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
30. Kauffman SA. 1993. The origins of order: self-organization and selection in evolution. Oxford University Press, Oxford, UK.
31. Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW. 2015. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161: 1187-1201.
32. Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA. 2015. The technology and biology of single-cell RNA sequencing. Mol Cell 58: 610-620.
33. Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, et al. 2014. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516: 56-61.
34. Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, Keren-Shaul H, Mildner A, Winter D, Jung S, et al. 2014. Chromatin state dynamics during blood formation. Science 345: 943-949.
35. Larsson C, Grundberg I, Söderberg O, Nilsson M. 2010. In situ detection and genotyping of individual mRNA molecules. Nat Methods 7: 395-397.
36. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, et al. 2014. Highly multiplexed subcellular RNA sequencing in situ. Science 343: 1360-1363.
37. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
38. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
39. Lubeck E, Cai L. 2012. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods 9: 743-748.
40. Macaulay IC, HaertyW, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, et al. 2015. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods 12: 519-522.
41. Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, et al. 2015. Highly parallel genome- wide expression profiling of individual cells using nanoliter droplets. Cell 161: 1202-1214.
42. Magwene PM, Lizardi P, Kim J. 2003. Reconstructing the temporal ordering of biological samples using microarray data. Bioinformatics 19: 842-850.
43. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
44. Mikkelsen TS, Manching K, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
45. Moignard V, Macaulay IC, Swiers G, Buettner F, Schütte J, Calero-Nieto FJ, Kinston S, Joshi A, Hannah R, Theis FJ, et al. 2013. Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat Cell Biol 15: 363-372.
46. Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, Buettner F, Macaulay IC, Jawaid W, Diamanti E, et al. 2015. Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol 33: 269-276.
47. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
48. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
49. Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, DeanW, Laue ED, Tanay A, Fraser P. 2013. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502: 59-64.
50. Nakamura T, Yabuta Y, Okamoto I, Aramaki S, Yokobayashi S, Kurimoto K, Sekiguchi K, Nakagawa M, Yamamoto T, Saitou M. 2015. SC3-seq: a method for highly parallel and quantitative measurement of singlecell gene expression. Nucleic Acids Res 43: e60.
51. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, et al. 2011. Tumour evolution inferred by single-cell sequencing. Nature 472: 90-94.
52. Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, FoleySW,Wu AR, Churchman LS, Singh A, Raj A. 2015. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Mol Cell 58: 1-15.
53. Picelli S, Faridani OR, Björklund AK, Winberg G, Sagasser S, Sandberg R. 2014. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9: 171-181.
54. Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, Li N, Szpankowski L, Fowler B, Chen P, et al. 2014. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol 32: 1-9.
55. Qiu P, Gentles AJ, Plevritis SK. 2011. Discovering biological progression underlying microarray samples. PLoS Comput Biol 7: e1001123.
56. Ramsköld D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, Daniels GA, Khrebtukova I, Loring JF, Laurent LC, et al. 2012. Full-length mRNASeq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 30: 777-782.
57. Rekhtman N, Radparvar F, Evans T, Skoultchi AI. 1999. Direct interaction of hematopoietic transcription factors PU.1 and GATA-1: functional antagonism in erythroid cells. Genes Dev 13: 1398-1411.
58. Saliba AE, Westermann AJ, Gorski SA, Vogel J. 2014. Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res 42: 8845-8860.
59. Satija R, Farrell JA, Gennert D, Schier AF, Regev A. 2015. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol 33: 495-502.
60. Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, et al. 2013. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498: 236-240.
61. Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, et al. 2014. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510: 363-369.
62. Simpson EH. 1951. The interpretation of interaction in contingency tables. J R Stat Soc Series B Stat Methodol 13: 238-241.
63. Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G. 2014. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat Methods 11: 817-820.
64. Sprinzak D, Lakhanpal A, LeBon L, Santat LA, Fontes ME, Anderson GA, Garcia-Ojalvo J, Elowitz MB. 2010. Cis-interactions between Notch and Delta generate mutually exclusive signalling states. Nature 465: 86-90.
65. Stegle O, Teichmann SA, Marioni JC. 2015. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet 16: 133-145.
66. Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, et al. 2013. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 154: 888-903.
67. Strahl BD, Allis CD. 2000. The language of covalent histone modifications. Nature 403: 41-45.
68. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, et al. 2009. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6: 377-382.
69. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. 2014. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 32: 381-386.
70. Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, Espinoza FH, Desai TJ, Krasnow MA, Quake SR. 2014. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509: 371-375.
71. Waddington CH. 1957. The strategy of the genes: a discussion of some aspects of theoretical biology. Allen & Unwin, London.
72. Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, et al. 2013. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 11: 41-46.
73. Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, et al. 2013. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature 500: 593-597.