Single-Cell DNA-Seq and RNA-Seq in Cancer Using the C1 System

Masahide Seki; Ayako Suzuki; Sarun Sereewattanawoot; Yutaka Suzuki

doi:10.1007/978-981-13-6037-4_3

Single-Cell DNA-Seq and RNA-Seq in Cancer Using the C1 System

Adv Exp Med Biol. 2019:1129:27-50. doi: 10.1007/978-981-13-6037-4_3.

Authors

Masahide Seki¹, Ayako Suzuki², Sarun Sereewattanawoot², Yutaka Suzuki²

Affiliations

¹ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan. [email protected].
² Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

PMID: 30968359
DOI: 10.1007/978-981-13-6037-4_3

Abstract

Heterogeneous phenotypes of cancer cells enable them to adapt to various environments. The heterogeneity results from diversity of genome, transcriptome, and epigenome at a single-cell level. The C1 system can automatically perform single-cell capture and whole genome amplification (WGA) or whole transcription amplification (WTA) by MDA or Smart-Seq, respectively. Here, we describe the protocols for WGA and WTA from a single cell by using the C1 system and the protocols for sequence library preparation from amplified gDNA and cDNA. We also described about the computational analysis for single-cell data of cancer.

Keywords: C1 system; Cancer; Fusion gene; MDA; SNP; SNV; Smart-Seq; scExome-Seq; scRNA-Seq; scWGS.

Publication types

Review

MeSH terms

Epigenomics
Humans
Neoplasms / genetics*
Nucleic Acid Amplification Techniques / methods*
Sequence Analysis, DNA / methods*
Sequence Analysis, RNA / methods*
Single-Cell Analysis / methods*
Transcriptome