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

  • Masahide SekiEmail author
  • Ayako Suzuki
  • Sarun Sereewattanawoot
  • Yutaka Suzuki
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1129)

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

Cancer C1 system scWGS scExome-Seq scRNA-Seq MDA Smart-Seq SNV SNP Fusion gene 

Notes

Acknowledgments

We would like to express our gratitude to Y Kuze, T Horiuchi, K Kunigo, Y Ishikawa, and K Imamura for helpful advice in writing this manuscript. This work was supported by MEXT KAKENHI Grant Number 221S0002.

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Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Masahide Seki
    • 1
    Email author
  • Ayako Suzuki
    • 1
  • Sarun Sereewattanawoot
    • 1
  • Yutaka Suzuki
    • 1
  1. 1.Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan

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