Single-cell Sequencing Techniques from Individual to Multiomics Analyses

Overview

Journal Exp Mol Med

Specialties Biochemistry
Molecular Biology

Date 2020 Sep 15

PMID 32929221

Citations 116

Authors

Yukie Kashima

Yoshitaka Sakamoto

Keiya Kaneko

Masahide Seki

Yutaka Suzuki

Ayako Suzuki

Affiliations

Soon will be listed here.

Abstract

Here, we review single-cell sequencing techniques for individual and multiomics profiling in single cells. We mainly describe single-cell genomic, epigenomic, and transcriptomic methods, and examples of their applications. For the integration of multilayered data sets, such as the transcriptome data derived from single-cell RNA sequencing and chromatin accessibility data derived from single-cell ATAC-seq, there are several computational integration methods. We also describe single-cell experimental methods for the simultaneous measurement of two or more omics layers. We can achieve a detailed understanding of the basic molecular profiles and those associated with disease in each cell by utilizing a large number of single-cell sequencing techniques and the accumulated data sets.

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References

Regev A, Teichmann S, Lander E, Amit I, Benoist C, Birney E . The Human Cell Atlas. Elife. 2017; 6. PMC: 5762154. DOI: 10.7554/eLife.27041. View

Kashima Y, Suzuki A, Suzuki Y . An Informative Approach to Single-Cell Sequencing Analysis. Adv Exp Med Biol. 2019; 1129:81-96. DOI: 10.1007/978-981-13-6037-4_6. View

Ramskold D, Luo S, Wang Y, Li R, Deng Q, Faridani O . Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol. 2012; 30(8):777-82. PMC: 3467340. DOI: 10.1038/nbt.2282. View

Picelli S, Bjorklund A, Faridani O, Sagasser S, Winberg G, Sandberg R . Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods. 2013; 10(11):1096-8. DOI: 10.1038/nmeth.2639. View

Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno K, Imai T . Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol. 2013; 14(4):R31. PMC: 4054835. DOI: 10.1186/gb-2013-14-4-r31. View

Hashimshony T, Wagner F, Sher N, Yanai I . CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012; 2(3):666-73. DOI: 10.1016/j.celrep.2012.08.003. View

Hayashi T, Ozaki H, Sasagawa Y, Umeda M, Danno H, Nikaido I . Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs. Nat Commun. 2018; 9(1):619. PMC: 5809388. DOI: 10.1038/s41467-018-02866-0. View

Macosko E, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M . Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214. PMC: 4481139. DOI: 10.1016/j.cell.2015.05.002. View

Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M . Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods. 2017; 14(10):955-958. PMC: 5623139. DOI: 10.1038/nmeth.4407. View

10.

Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S . Mapping the Mouse Cell Atlas by Microwell-Seq. Cell. 2018; 172(5):1091-1107.e17. DOI: 10.1016/j.cell.2018.02.001. View

11.

Hashimoto S . Nx1-Seq (Well Based Single-Cell Analysis System). Adv Exp Med Biol. 2019; 1129:51-61. DOI: 10.1007/978-981-13-6037-4_4. View

12.

Gierahn T, Wadsworth 2nd M, Hughes T, Bryson B, Butler A, Satija R . Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods. 2017; 14(4):395-398. PMC: 5376227. DOI: 10.1038/nmeth.4179. View

13.

Cao J, Packer J, Ramani V, Cusanovich D, Huynh C, Daza R . Comprehensive single-cell transcriptional profiling of a multicellular organism. Science. 2017; 357(6352):661-667. PMC: 5894354. DOI: 10.1126/science.aam8940. View

14.

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim D, Hill A . The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019; 566(7745):496-502. PMC: 6434952. DOI: 10.1038/s41586-019-0969-x. View

15.

Kouno T, Moody J, Kwon A, Shibayama Y, Kato S, Huang Y . C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun. 2019; 10(1):360. PMC: 6341120. DOI: 10.1038/s41467-018-08126-5. View

16.

Matsunaga H, Goto M, Arikawa K, Shirai M, Tsunoda H, Huang H . A highly sensitive and accurate gene expression analysis by sequencing ("bead-seq") for a single cell. Anal Biochem. 2014; 471:9-16. DOI: 10.1016/j.ab.2014.10.011. View

17.

Kashima Y, Suzuki A, Liu Y, Hosokawa M, Matsunaga H, Shirai M . Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response. Sci Rep. 2018; 8(1):3482. PMC: 5823859. DOI: 10.1038/s41598-018-21161-y. View

18.

Patel A, Tirosh I, Trombetta J, Shalek A, Gillespie S, Wakimoto H . Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014; 344(6190):1396-401. PMC: 4123637. DOI: 10.1126/science.1254257. View

19.

Venteicher A, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin M . Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science. 2017; 355(6332). PMC: 5519096. DOI: 10.1126/science.aai8478. View

20.

Tirosh I, Venteicher A, Hebert C, Escalante L, Patel A, Yizhak K . Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016; 539(7628):309-313. PMC: 5465819. DOI: 10.1038/nature20123. View