List of single cell omics methods

A list of more than 100 different single cell sequencing (omics) methods have been published.[1] The large majority of methods are paired with short-read sequencing technologies, although some of them are compatible with long read sequencing.

List
Method Reference Sequencing Mode Early Estimate Late Estimate
Tang method [2] Short Reads 2008 2009
CyTOF [3] Short Reads 2011 2012
STRT-seq / C1 [4] Short Reads 2011 2012
SMART-seq [5] Short Reads 2012 2013
CEL-seq [6] Short Reads 2012 2013
Quartz-Seq [7] Short Reads 2012 2013
PMA / SMA [8] Short Reads 2012 2013
scBS-seq [9] Short Reads 2013 2014
AbPair [10] Short Reads 2014 2014
MARS-seq [11] Short Reads 2014 2015
DR-seq [12] Short Reads 2014 2015
G&T-Seq [13] Short Reads 2014 2015
SCTG [14] Short Reads 2014 2015
SIDR-seq [15] Short Reads 2014 2015
sci-ATAC-seq [16] Short Reads 2014 2015
Hi-SCL [17] Short Reads 2015 2015
SUPeR-seq [18] Short Reads 2015 2015
Drop-Chip [19] Short Reads 2015 2015
CytoSeq [20] Short Reads 2015 2016
inDrop [21] Short Reads 2015 2016
sc-GEM [22] Short Reads 2015 2016
scTrio-seq [23] Short Reads 2015 2016
scM&T-seq [24] Short Reads 2015 2016
PLAYR [25] Short Reads 2015 2016
Genshaft-et-al-2016 [26] Short Reads 2015 2016
Darmanis-et-al-2016 [27] Short Reads 2015 2016
CRISP-seq [28] Short Reads 2015 2016
scGESTALT [29] Short Reads 2015 2016
CEL-Seq2 / C1 [30] Short Reads 2015 2016
STRT-seq-2i [31] Short Reads 2016 2017
RNAseq @10xgenomics [32] Short Reads 2016 2017
RNAseq / Gene Expression @nanostringtech [33] Short Reads 2016 2017
sc Targeted Gene Expression @fluidigm [34] Short Reads 2016 2017
scTCR Wafergen [35] Short Reads 2016 2017
CROP-seq [36] Short Reads 2016 2017
SiC-seq [37] Short Reads 2016 2017
mcSCRB-seq [38] Short Reads 2016 2017
Patch-seq [39] Short Reads 2016 2017
Geo-seq [40] Short Reads 2016 2017
scNOMe-seq [41] Short Reads 2016 2017
scCOOL-seq [42] Short Reads 2016 2017
CUT&Run [43] Short Reads 2016 2017
MATQ-seq [44] Short Reads 2016 2017
Quartz-Seq2 [45] Short Reads 2017 2018
Seq-Well [46] Short Reads 2017 2018
DroNC-Seq [47] Short Reads 2017 2018
sci-RNA-seq [48] Short Reads 2017 2018
scATAC @10xgenomics [49] Short Reads 2017 2018
scVDJ @10xgenomics [50] Short Reads 2017 2018
scNMT triple omics [51] Short Reads 2017 2018
SPLIT-seq Split Biosciences [52] Short Reads 2017 2018
CITE-Seq [53] Short Reads 2017 2018
scMNase-seq [54] Short Reads 2017 2018
Chaligne-et-al-2018 [55] Short Reads 2017 2018
LINNAEUS [56] Short Reads 2017 2018
TracerSeq [57] Short Reads 2017 2018
CellTag [58] Short Reads 2017 2018
ScarTrace [59] Short Reads 2017 2018
scRNA-Seq Dolomite Bio [60] Short Reads 2017 2018
Trac-looping [61] Short Reads 2017 2018
Perturb-ATAC [62] Short Reads 2018 2019
scMethylation [63] Short Reads 2018 2019
scHiC [64] Short Reads 2018 2019
Multiplex Droplet scRNAseq [65] Short Reads 2018 2019
sci-CAR [66] Short Reads 2018 2019
C1 CAGE single cell [67] Short Reads 2018 2019
sc paired microRNA-mRNA [68] Short Reads 2018 2019
scCAT-seq [69] Short Reads 2018 2019
REAP-seq @fluidigm [70] Short Reads 2018 2019
scCC [71] Short Reads 2018 2019
yscRNA-SEQ [72] Short Reads 2018 2019
TARGET-seq [73] Short Reads 2018 2019
MULTI-seq [74] Short Reads 2018 2019
snRNA-seq [75] Short Reads 2018 2019
sci-RNA-seq3 [76] Short Reads 2018 2019
BRIF-seq [77] Short Reads 2018 2019
Drop-seq Dolomite Bio [60] Short Reads 2018 2019
Slide-seq [78] Short Reads 2018 2019
CUT&Tag [79] Short Reads 2018 2019
CellTagging [80] Short Reads 2018 2019
DART-Seq [81] Short Reads 2018 2019
scDamID&T [82] Short Reads 2018 2019
ACT-seq [83] Short Reads 2018 2019
Sci-Hi-C [84] Short Reads 2018 2019
Slide-seq [85] Short Reads 2018 2019
Simplified-Drop-seq [86] Short Reads 2018 2019
scChIC-seq [87] Short Reads 2018 2019
Dip-C [88] Short Reads 2018 2019
CoBATCH [89] Short Reads 2018 2019
Convert-seq [90] Short Reads 2018 2019
Droplet-based scATAC-seq [91] Short Reads 2018 2019
ECCITE-seq [92] Short Reads 2018 2019
dsciATAC-seq [91] Short Reads 2018 2019
CLEVER-seq [93] Short Reads 2018 2019
scISOr-Seq [94] Short Reads 2018 2019
MARS-seq2.0 [95] Short Reads 2018 2019
nano-NOMe [96] Long Reads 2018 2019
MeSMLR-seq [97] Long Reads 2018 2019
SMAC-seq [98] Long Reads 2018 2019
MoonTag/SunTag [99] Short Reads 2018 2019
SCoPE2 [100] Short Reads 2018 2019
sci-fate [101] Short Reads 2018 2019
µDamID [102] Short Reads 2018 2019
Methyl-HiC [103] Short Reads 2018 2019
RAGE-seq [104] Long Reads 2018 2019
Paired-Seq [105] Short Reads 2018 2019
Tn5Prime [106] Short Reads 2018 2019
NanoPARE [107] Short Reads 2018 2019
BART-Seq [108] Short Reads 2018 2019
scDam&T-seq [109] Short Reads 2018 2019
itChIP-seq [110] Short Reads 2018 2019
SNARE-seq [111] Short Reads 2018 2019
ASTAR-seq [112] Short Reads 2018 2019
sci-Plex [113] Short Reads 2018 2019
MIX-Seq [114] Short Reads 2018 2019
microSPLiT [115] Short Reads 2018 2019
PAIso-seq [116] Short Reads 2018 2019
FIN-Seq [117] Short Reads 2018 2019
LIBRA-seq [118] Short Reads 2018 2019
scifi-RNA-seq [119] Short Reads 2018 2019

References
  1. "Single-Cell-Omics.v2.3.13 @albertvilella". Google Docs. Retrieved 2020-01-01.
  2. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. (May 2009). "mRNA-Seq whole-transcriptome analysis of a single cell". Nature Methods. 6 (5): 377–82. doi:10.1038/nmeth.1315. PMID 19349980. S2CID 16570747.
  3. "Fluidigm | Single-Cell Advances". www.fluidigm.com.
  4. Hashimshony T, Wagner F, Sher N, Yanai I (September 2012). "CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification". Cell Reports. 2 (3): 666–73. doi:10.1016/j.celrep.2012.08.003. PMID 22939981.
  5. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. (February 2014). "Quantitative single-cell RNA-seq with unique molecular identifiers". Nature Methods. 11 (2): 163–6. doi:10.1038/nmeth.2772. PMID 24363023. S2CID 6765530.
  6. Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. (February 2014). "Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types". Science. 343 (6172): 776–9. Bibcode:2014Sci...343..776J. doi:10.1126/science.1247651. PMC 4412462. PMID 24531970.
  7. Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR (April 2013). "Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity". Genome Biology. 14 (4): R31. doi:10.1186/gb-2013-14-4-r31. PMC 4054835. PMID 23594475.
  8. Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, et al. (January 2013). "Two methods for full-length RNA sequencing for low quantities of cells and single cells". Proceedings of the National Academy of Sciences of the United States of America. 110 (2): 594–9. Bibcode:2013PNAS..110..594P. doi:10.1073/pnas.1217322109. PMC 3545756. PMID 23267071.
  9. Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, et al. (August 2014). "Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity". Nature Methods. 11 (8): 817–820. doi:10.1038/nmeth.3035. PMC 4117646. PMID 25042786.
  10. Briggs AW, Goldfless SJ, Timberlake S, Belmont BJ, Clouser CR, Koppstein D, et al. (May 5, 2017). "Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion". bioRxiv: 134841. doi:10.1101/134841.
  11. Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R (November 2013). "Smart-seq2 for sensitive full-length transcriptome profiling in single cells". Nature Methods. 10 (11): 1096–8. doi:10.1038/nmeth.2639. PMID 24056875. S2CID 6356570.
  12. Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A (March 2015). "Integrated genome and transcriptome sequencing of the same cell". Nature Biotechnology. 33 (3): 285–289. doi:10.1038/nbt.3129. PMC 4374170. PMID 25599178.
  13. Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, et al. (June 2015). "G&T-seq: parallel sequencing of single-cell genomes and transcriptomes". Nature Methods. 12 (6): 519–22. doi:10.1038/nmeth.3370. PMID 25915121. S2CID 969246.
  14. Li W, Calder RB, Mar JC, Vijg J (February 2015). "Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles". Mutation Research. 772: 55–62. doi:10.1016/j.mrfmmm.2015.01.002. PMC 4342853. PMID 25733965.
  15. Han KY, Kim KT, Joung JG, Son DS, Kim YJ, Jo A, et al. (January 2018). "SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells". Genome Research. 28 (1): 75–87. doi:10.1101/gr.223263.117. PMC 5749184. PMID 29208629.
  16. Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, et al. (May 2015). "Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing". Science. 348 (6237): 910–4. Bibcode:2015Sci...348..910C. doi:10.1126/science.aab1601. PMC 4836442. PMID 25953818.
  17. Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, et al. (January 1, 2015). "High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics". PLOS ONE. 10 (5): e0116328. Bibcode:2015PLoSO..1016328R. doi:10.1371/journal.pone.0116328. PMC 4441486. PMID 26000628.
  18. Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F, Huang Y (July 2015). "Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos". Genome Biology. 16 (1): 148. doi:10.1186/s13059-015-0706-1. PMC 4511241. PMID 26201400.
  19. "Drop-Chip". pubs.broadinstitute.org.
  20. Fan HC, Fu GK, Fodor SP (February 2015). "Expression profiling. Combinatorial labeling of single cells for gene expression cytometry". Science. 347 (6222): 1258367. doi:10.1126/science.1258367. PMID 25657253. S2CID 5493175.
  21. Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, et al. (May 2015). "Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells". Cell. 161 (5): 1187–1201. doi:10.1016/j.cell.2015.04.044. PMC 4441768. PMID 26000487.
  22. Cheow LF, Courtois ET, Tan Y, Viswanathan R, Xing Q, Tan RZ, et al. (October 2016). "Single-cell multimodal profiling reveals cellular epigenetic heterogeneity". Nature Methods. 13 (10): 833–6. doi:10.1038/nmeth.3961. PMID 27525975. S2CID 3531201.
  23. Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, et al. (March 2016). "Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas". Cell Research. 26 (3): 304–19. doi:10.1038/cr.2016.23. PMC 4783472. PMID 26902283.
  24. Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, et al. (March 2016). "Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity". Nature Methods. 13 (3): 229–232. doi:10.1038/nmeth.3728. PMC 4770512. PMID 26752769.
  25. Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF (March 2016). "Highly multiplexed simultaneous detection of RNAs and proteins in single cells". Nature Methods. 13 (3): 269–75. doi:10.1038/nmeth.3742. PMC 4767631. PMID 26808670.
  26. Genshaft AS, Li S, Gallant CJ, Darmanis S, Prakadan SM, Ziegler CG, et al. (September 2016). "Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction". Genome Biology. 17 (1): 188. doi:10.1186/s13059-016-1045-6. PMC 5027636. PMID 27640647.
  27. Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, et al. (October 2017). "Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma". Cell Reports. 21 (5): 1399–1410. doi:10.1016/j.celrep.2017.10.030. PMC 5810554. PMID 29091775.
  28. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, et al. (December 2016). "Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq". Cell. 167 (7): 1883–1896.e15. doi:10.1016/j.cell.2016.11.039. PMID 27984734.
  29. Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, et al. (June 2018). "Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain". Nature Biotechnology. 36 (5): 442–450. doi:10.1038/nbt.4103. PMC 5938111. PMID 29608178.
  30. Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, et al. (April 2016). "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq". Genome Biology. 17 (1): 77. doi:10.1186/s13059-016-0938-8. PMC 4848782. PMID 27121950.
  31. Hochgerner H, Lönnerberg P, Hodge R, Mikes J, Heskol A, Hubschle H, et al. (November 2017). "STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array". Scientific Reports. 7 (1): 16327. Bibcode:2017NatSR...716327H. doi:10.1038/s41598-017-16546-4. PMC 5703850. PMID 29180631.
  32. "Single Cell RNA-Seq". 10x Genomic.
  33. "nCounter® Technology". NanoString Technologies.
  34. "Fluidigm | Consumables | Single-Cell Targeted Gene Expression". www.fluidigm.com.
  35. Inc, WaferGen Bio-systems. "WaferGen Presents Single-Cell T-Cell Receptor Sequencing Results Using the ICELL8™ Single-Cell System at the 2016 Single Cell Genomics Meeting". www.prnewswire.com.
  36. Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, et al. (March 2017). "Pooled CRISPR screening with single-cell transcriptome readout". Nature Methods. 14 (3): 297–301. doi:10.1038/nmeth.4177. PMC 5334791. PMID 28099430.
  37. Lan F, Demaree B, Ahmed N, Abate AR (July 2017). "Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding". Nature Biotechnology. 35 (7): 640–646. doi:10.1038/nbt.3880. PMC 5531050. PMID 28553940.
  38. Bagnoli JW, Ziegenhain C, Janjic A, Wange LE, Vieth B, Parekh S, et al. (October 18, 2017). "mcSCRB-seq: sensitive and powerful single-cell RNA sequencing". bioRxiv: 188367. doi:10.1101/188367.
  39. Cadwell CR, Sandberg R, Jiang X, Tolias AS (July 2017). "Q&A: using Patch-seq to profile single cells". BMC Biology. 15 (1): 58. doi:10.1186/s12915-017-0396-0. PMC 5499043. PMID 28679385.
  40. Chen J, Suo S, Tam PP, Han JJ, Peng G, Jing N (March 2017). "Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq". Nature Protocols. 12 (3): 566–580. doi:10.1038/nprot.2017.003. PMID 28207000.
  41. Pott S (June 2017). Ren B (ed.). "Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells". eLife. 6: e23203. doi:10.7554/eLife.23203. PMC 5487215. PMID 28653622.
  42. Guo F, Li L, Li J, Wu X, Hu B, Zhu P, et al. (August 2017). "Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells". Cell Research. 27 (8): 967–988. doi:10.1038/cr.2017.82. PMC 5539349. PMID 28621329.
  43. Skene PJ, Henikoff S (January 2017). Reinberg D (ed.). "An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites". eLife. 6: e21856. doi:10.7554/eLife.21856. PMC 5310842. PMID 28079019.
  44. Sheng K, Cao W, Niu Y, Deng Q, Zong C (March 2017). "Effective detection of variation in single-cell transcriptomes using MATQ-seq". Nature Methods. 14 (3): 267–270. doi:10.1038/nmeth.4145. PMID 28092691. S2CID 582788.
  45. Sasagawa Y, Danno H, Takada H, Ebisawa M, Tanaka K, Hayashi T, et al. (March 2018). "Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads". Genome Biology. 19 (1): 29. doi:10.1186/s13059-018-1407-3. PMC 5845169. PMID 29523163.
  46. Gierahn TM, Wadsworth MH, Hughes TK, Bryson BD, Butler A, Satija R, et al. (April 2017). "Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput". Nature Methods. 14 (4): 395–398. doi:10.1038/nmeth.4179. hdl:1721.1/113430. PMC 5376227. PMID 28192419.
  47. Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, et al. (October 2017). "Massively parallel single-nucleus RNA-seq with DroNc-seq". Nature Methods. 14 (10): 955–958. doi:10.1038/nmeth.4407. PMC 5623139. PMID 28846088.
  48. Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, et al. (August 2017). "Comprehensive single-cell transcriptional profiling of a multicellular organism". Science. 357 (6352): 661–667. Bibcode:2017Sci...357..661C. doi:10.1126/science.aam8940. PMC 5894354. PMID 28818938.
  49. https://www.10xgenomics.com/solutions/single-cell-atac/
  50. https://www.10xgenomics.com/solutions/vdj/
  51. Argelaguet R, Mohammed H, Clark SJ, Stapel LC, Krueger C, Kapourani C, et al. (January 13, 2019). "Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification". bioRxiv: 519207. doi:10.1101/519207.
  52. Rosenberg AB, Roco CM, Muscat RA, Kuchina A, Sample P, Yao Z, et al. (April 2018). "Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding". Science. 360 (6385): 176–182. Bibcode:2018Sci...360..176R. doi:10.1126/science.aam8999. PMID 29545511.
  53. Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, et al. (September 2017). "Simultaneous epitope and transcriptome measurement in single cells". Nature Methods. 14 (9): 865–868. doi:10.1038/nmeth.4380. PMC 5669064. PMID 28759029.
  54. Lai B, Gao W, Cui K, Xie W, Tang Q, Jin W, et al. (October 2018). "Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing". Nature. 562 (7726): 281–285. Bibcode:2018Natur.562..281L. doi:10.1038/s41586-018-0567-3. PMID 30258225. S2CID 52841785.
  55. Nam AS, Kim K, Chaligne R, Izzo F, Ang C, Abu-Zeinah G, et al. (October 16, 2018). "High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations". bioRxiv: 444687. doi:10.1101/444687.
  56. Spanjaard B, Hu B, Mitic N, Olivares-Chauvet P, Janjuha S, Ninov N, Junker JP (June 2018). "Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars". Nature Biotechnology. 36 (5): 469–473. doi:10.1038/nbt.4124. PMC 5942543. PMID 29644996.
  57. Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM (June 2018). "Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo". Science. 360 (6392): 981–987. Bibcode:2018Sci...360..981W. doi:10.1126/science.aar4362. PMC 6083445. PMID 29700229.
  58. Guo C, Kong W, Kamimoto K, Rivera-Gonzalez GC, Yang X, Kirita Y, Morris SA (May 2019). "CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics". Genome Biology. 20 (1): 90. doi:10.1186/s13059-019-1699-y. PMC 6509836. PMID 31072405.
  59. Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A (April 2018). "Whole-organism clone tracing using single-cell sequencing". Nature. 556 (7699): 108–112. Bibcode:2018Natur.556..108A. doi:10.1038/nature25969. PMID 29590089. S2CID 4633026.
  60. "Nadia Instrument". Dolomite Bio.
  61. Lai B, Tang Q, Jin W, Hu G, Wangsa D, Cui K, et al. (September 2018). "Trac-looping measures genome structure and chromatin accessibility". Nature Methods. 15 (9): 741–747. doi:10.1038/s41592-018-0107-y. PMC 7212307. PMID 30150754.
  62. Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, et al. (January 2019). "Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks". Cell. 176 (1–2): 361–376.e17. doi:10.1016/j.cell.2018.11.022. PMC 6329648. PMID 30580963.
  63. Karemaker ID, Vermeulen M (September 2018). "Single-Cell DNA Methylation Profiling: Technologies and Biological Applications". Trends in Biotechnology. 36 (9): 952–965. doi:10.1016/j.tibtech.2018.04.002. PMID 29724495.
  64. de Wit E (May 2017). "Capturing heterogeneity: single-cell structures of the 3D genome". Nature Structural & Molecular Biology. 24 (5): 437–438. doi:10.1038/nsmb.3404. PMID 28471429. S2CID 5132000.
  65. Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, et al. (January 2018). "Multiplexed droplet single-cell RNA-sequencing using natural genetic variation". Nature Biotechnology. 36 (1): 89–94. doi:10.1038/nbt.4042. PMC 5784859. PMID 29227470.
  66. Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, et al. (September 2018). "Joint profiling of chromatin accessibility and gene expression in thousands of single cells". Science. 361 (6409): 1380–1385. Bibcode:2018Sci...361.1380C. doi:10.1126/science.aau0730. PMC 6571013. PMID 30166440.
  67. Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang Y, et al. (January 2019). "C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution". Nature Communications. 10 (1): 360. Bibcode:2019NatCo..10..360K. doi:10.1038/s41467-018-08126-5. PMC 6341120. PMID 30664627.
  68. Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, et al. (January 2019). "Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation". Nature Communications. 10 (1): 95. Bibcode:2019NatCo..10...95W. doi:10.1038/s41467-018-07981-6. PMC 6327095. PMID 30626865.
  69. Liu L, Liu C, Quintero A, Wu L, Yuan Y, Wang M, et al. (January 2019). "Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity". Nature Communications. 10 (1): 470. Bibcode:2019NatCo..10..470L. doi:10.1038/s41467-018-08205-7. PMC 6349937. PMID 30692544.
  70. Corporation, Fluidigm (January 31, 2019). "Fluidigm Introduces REAP-Seq for Multi-Omic Single-Cell Analysis on the C1". GlobeNewswire News Room.
  71. Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, et al. (February 1, 2019). "Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells". bioRxiv: 538553. doi:10.1101/538553. PMID 32710817.
  72. Nadal-Ribelles M, Islam S, Wei W, Latorre P, Nguyen M, de Nadal E, et al. (April 2019). "Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations". Nature Microbiology. 4 (4): 683–692. doi:10.1038/s41564-018-0346-9. PMC 6433287. PMID 30718850.
  73. Rodriguez-Meira A, Buck G, Clark SA, Povinelli BJ, Alcolea V, Louka E, et al. (March 2019). "Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing". Molecular Cell. 73 (6): 1292–1305.e8. doi:10.1016/j.molcel.2019.01.009. PMC 6436961. PMID 30765193.
  74. McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, et al. (July 2019). "MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices". Nature Methods. 16 (7): 619–626. doi:10.1038/s41592-019-0433-8. PMC 6837808. PMID 31209384.
  75. Gaublomme JT, Li B, McCabe C, Knecht A, Yang Y, Drokhlyansky E, et al. (July 2019). "Nuclei multiplexing with barcoded antibodies for single-nucleus genomics". Nature Communications. 10 (1): 2907. Bibcode:2019NatCo..10.2907G. doi:10.1038/s41467-019-10756-2. PMC 6606589. PMID 31266958.
  76. "Mouse RNA Atlas". oncoscape.v3.sttrcancer.org.
  77. Li X, Chen L, Zhang Q, Sun Y, Li Q, Yan J (March 2019). "BRIF-Seq: Bisulfite-Converted Randomly Integrated Fragments Sequencing at the Single-Cell Level". Molecular Plant. 12 (3): 438–446. doi:10.1016/j.molp.2019.01.004. PMID 30639749.
  78. Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, et al. (March 2019). "Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution". Science. 363 (6434): 1463–1467. Bibcode:2019Sci...363.1463R. doi:10.1126/science.aaw1219. PMC 6927209. PMID 30923225.
  79. Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, et al. (April 2019). "CUT&Tag for efficient epigenomic profiling of small samples and single cells". Nature Communications. 10 (1): 1930. Bibcode:2019NatCo..10.1930K. doi:10.1038/s41467-019-09982-5. PMC 6488672. PMID 31036827.
  80. Biddy, Brent A. (March 7, 2019). "Single-cell mapping of lineage and identity via CellTagging". Protocols.io. doi:10.17504/protocols.io.yxifxke.
  81. Saikia M, Burnham P, Keshavjee SH, Wang MF, Heyang M, Moral-Lopez P, et al. (January 2019). "Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells". Nature Methods. 16 (1): 59–62. doi:10.1038/s41592-018-0259-9. PMC 6378878. PMID 30559431.
  82. Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, et al. (July 2019). "Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells". Nature Biotechnology. 37 (7): 766–772. doi:10.1038/s41587-019-0150-y. PMC 6609448. PMID 31209373.
  83. Carter B, Ku WL, Kang JY, Hu G, Perrie J, Tang Q, Zhao K (August 2019). "Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)". Nature Communications. 10 (1): 3747. Bibcode:2019NatCo..10.3747C. doi:10.1038/s41467-019-11559-1. PMC 6702168. PMID 31431618.
  84. Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, et al. (September 2019). "Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells". Methods. 170: 61–68. doi:10.1016/j.ymeth.2019.09.012. PMC 6949367. PMID 31536770.
  85. Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, et al. (March 2019). "Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution". Science. 363 (6434): 1463–1467. Bibcode:2019Sci...363.1463R. doi:10.1126/science.aaw1219. PMC 6927209. PMID 30923225.
  86. Biočanin M, Bues J, Dainese R, Amstad E, Deplancke B (April 2019). "Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip". Lab on a Chip. 19 (9): 1610–1620. doi:10.1039/C9LC00014C. PMID 30920557.
  87. Ku WL, Nakamura K, Gao W, Cui K, Hu G, Tang Q, et al. (April 2019). "Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification". Nature Methods. 16 (4): 323–325. doi:10.1038/s41592-019-0361-7. PMC 7187538. PMID 30923384.
  88. Tan L, Xing D, Daley N, Xie XS (April 2019). "Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems". Nature Structural & Molecular Biology. 26 (4): 297–307. doi:10.1038/s41594-019-0205-2. PMID 30936528. S2CID 89616808.
  89. Wang Q, Xiong H, Ai S, Yu X, Liu Y, Zhang J, He A (October 2019). "CoBATCH for High-Throughput Single-Cell Epigenomic Profiling". Molecular Cell. 76 (1): 206–216.e7. doi:10.1016/j.molcel.2019.07.015. PMID 31471188.
  90. Luginbühl J, Kouno T, Nakano R, Chater TE, Sivaraman DM, Kishima M, et al. (April 5, 2019). "Decoding neuronal diversity by single-cell Convert-seq". bioRxiv: 600239. doi:10.1101/600239.
  91. Lareau CA, Duarte FM, Chew JG, Kartha VK, Burkett ZD, Kohlway AS, et al. (August 2019). "Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility". Nature Biotechnology. 37 (8): 916–924. doi:10.1038/s41587-019-0147-6. PMID 31235917. S2CID 195329871.
  92. Mimitou EP, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, et al. (May 2019). "Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells". Nature Methods. 16 (5): 409–412. doi:10.1038/s41592-019-0392-0. PMC 6557128. PMID 31011186.
  93. Zhu C, Gao Y, Peng J, Tang F, Yi C (January 1, 2019). "Single-Cell 5fC Sequencing". Single Cell Methods. Methods in Molecular Biology. 1979. Clifton, N.J. pp. 251–267. doi:10.1007/978-1-4939-9240-9_16. ISBN 978-1-4939-9239-3. PMID 31028643.
  94. Russell AB, Elshina E, Kowalsky JR, Te Velthuis AJ, Bloom JD (July 2019). "Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity". Journal of Virology. 93 (14). doi:10.1128/JVI.00500-19. PMC 6600203. PMID 31068418.
  95. Keren-Shaul H, Kenigsberg E, Jaitin DA, David E, Paul F, Tanay A, Amit I (June 2019). "MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing". Nature Protocols. 14 (6): 1841–1862. doi:10.1038/s41596-019-0164-4. PMID 31101904. S2CID 156055842.
  96. Lee I, Razaghi R, Gilpatrick T, Molnar M, Sadowski N, Simpson JT, et al. (February 2, 2019). "Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing". bioRxiv: 504993. doi:10.1101/504993.
  97. Wang Y, Wang A, Liu Z, Thurman AL, Powers LS, Zou M, et al. (August 2019). "Single-molecule long-read sequencing reveals the chromatin basis of gene expression". Genome Research. 29 (8): 1329–1342. doi:10.1101/gr.251116.119. PMC 6673713. PMID 31201211.
  98. Shipony Z, Marinov GK, Swaffer MP, Sinott-Armstrong NA, Skotheim JM, Kundaje A, et al. (December 22, 2018). "Long-range single-molecule mapping of chromatin accessibility in eukaryotes". bioRxiv. 17 (3): 319–327. doi:10.1101/504662. PMID 32042188.
  99. Boersma S, Khuperkar D, Verhagen BM, Sonneveld S, Grimm JB, Lavis LD, Tanenbaum ME (July 2019). "Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding". Cell. 178 (2): 458–472.e19. doi:10.1016/j.cell.2019.05.001. PMC 6630898. PMID 31178119.
  100. Specht H, Emmott E, Koller T, Slavov N (June 9, 2019). "High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity". bioRxiv: 665307. doi:10.1101/665307.
  101. Cao J, Zhou W, Steemers F, Trapnell C, Shendure J (June 11, 2019). "Characterizing the temporal dynamics of gene expression in single cells with sci-fate". bioRxiv: 666081. doi:10.1101/666081.
  102. Altemose N, Maslan A, Lai A, White JA, Streets AM (July 18, 2019). "μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells". bioRxiv: 706903. doi:10.1101/706903.
  103. Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, et al. (October 2019). "Joint profiling of DNA methylation and chromatin architecture in single cells". Nature Methods. 16 (10): 991–993. doi:10.1038/s41592-019-0502-z. PMC 6765429. PMID 31384045.
  104. Singh M, Al-Eryani G, Carswell S, Ferguson JM, Blackburn J, Barton K, et al. (July 2019). "High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes". Nature Communications. 10 (1): 3120. Bibcode:2019NatCo..10.3120S. doi:10.1038/s41467-019-11049-4. PMC 6635368. PMID 31311926.
  105. Zhu C, Yu M, Huang H, Juric I, Abnousi A, Hu R, et al. (November 2019). "An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome". Nature Structural & Molecular Biology. 26 (11): 1063–1070. doi:10.1038/s41594-019-0323-x. PMC 7231560. PMID 31695190.
  106. Cole C, Byrne A, Beaudin AE, Forsberg EC, Vollmers C (June 2018). "Tn5Prime, a Tn5 based 5' capture method for single cell RNA-seq". Nucleic Acids Research. 46 (10): e62. doi:10.1093/nar/gky182. PMC 6007450. PMID 29548006.
  107. Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD (December 2018). "NanoPARE: parallel analysis of RNA 5' ends from low-input RNA". Genome Research. 28 (12): 1931–1942. doi:10.1101/gr.239202.118. PMC 6280765. PMID 30355603.
  108. Uzbas F, Opperer F, Sönmezer C, Shaposhnikov D, Sass S, Krendl C, et al. (August 2019). "BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis". Genome Biology. 20 (1): 155. doi:10.1186/s13059-019-1748-6. PMC 6683345. PMID 31387612.
  109. Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, et al. (July 2019). "Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells". Nature Biotechnology. 37 (7): 766–772. doi:10.1038/s41587-019-0150-y. PMC 6609448. PMID 31209373.
  110. Ai S, Xiong H, Li CC, Luo Y, Shi Q, Liu Y, et al. (September 2019). "Profiling chromatin states using single-cell itChIP-seq". Nature Cell Biology. 21 (9): 1164–1172. doi:10.1038/s41556-019-0383-5. PMID 31481796. S2CID 201815293.
  111. Chen S, Lake BB, Zhang K (December 2019). "High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell". Nature Biotechnology. 37 (12): 1452–1457. doi:10.1038/s41587-019-0290-0. PMC 6893138. PMID 31611697.
  112. Xing QR, Farran CE, Yi Y, Warrier T, Gautam P, Collins JJ, et al. (November 4, 2019). "Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility". bioRxiv: 829960. doi:10.1101/829960. PMID 32699019.
  113. Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, et al. (December 2019). "Massively multiplex chemical transcriptomics at single cell resolution". Science. 367 (6473): 45–51. doi:10.1126/science.aax6234. PMC 7289078. PMID 31806696.
  114. McFarland JM, Paolella BR, Warren A, Geiger-Schuller K, Shibue T, Rothberg M, et al. (December 8, 2019). "Multiplexed single-cell profiling of post-perturbation transcriptional responses to define cancer vulnerabilities and therapeutic mechanism of action". bioRxiv: 868752. doi:10.1101/868752.
  115. Kuchina A, Brettner LM, Paleologu L, Roco CM, Rosenberg AB, Carignano A, et al. (December 11, 2019). "Microbial single-cell RNA sequencing by split-pool barcoding". bioRxiv: 869248. doi:10.1101/869248.
  116. Liu Y, Nie H, Liu H, Lu F (November 2019). "Poly(A) inclusive RNA isoform sequencing (PAIso-seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails". Nature Communications. 10 (1): 5292. Bibcode:2019NatCo..10.5292L. doi:10.1038/s41467-019-13228-9. PMC 6876564. PMID 31757970.
  117. Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P (November 2019). "FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system". Nucleic Acids Research. 48 (1): e4. doi:10.1093/nar/gkz968. PMC 7145626. PMID 31728515.
  118. Setliff I, Shiakolas AR, Pilewski KA, Murji AA, Mapengo RE, Janowska K, et al. (December 2019). "High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity". Cell. 179 (7): 1636–1646.e15. doi:10.1016/j.cell.2019.11.003. PMC 7158953. PMID 31787378.
  119. Datlinger P, Rendeiro AF, Boenke T, Krausgruber T, Barreca D, Bock C (December 18, 2019). "Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing". bioRxiv: 2019.12.17.879304. doi:10.1101/2019.12.17.879304.
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