Combined Genome and Transcriptome (G&T) Sequencing of Single Cells

Methods Mol Biol. 2019:1979:319-362. doi: 10.1007/978-1-4939-9240-9_20.

Abstract

The simultaneous examination of a single cell's genome and transcriptome presents scientists with a powerful tool to study genetic variability and its effect on gene expression. In this chapter, we describe the library generation method for combined genome and transcriptome sequencing (G&T-seq) originally described by Macaulay et al. (Nat Protoc 11(11):2081-2103, 2016; Nat Methods 12(6):519-522, 2015). This includes some alterations we made to improve robustness of this process for both the novice user and laboratories that want to deploy this method at scale. Using this method, genomic DNA and full-length mRNA from single cells are separated, amplified, and converted into Illumina sequencer-compatible sequencing libraries.

Keywords: Copy number variation; Gene expression; Genome; MDA; NGS; SNV detection; Single cell; Transcriptome; WGA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / genetics
  • DNA Copy Number Variations
  • Gene Expression Profiling / methods*
  • Gene Library
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • RNA, Messenger / genetics
  • Sequence Analysis, DNA / methods
  • Single-Cell Analysis / methods*
  • Transcriptome
  • Whole Genome Sequencing / methods

Substances

  • RNA, Messenger
  • DNA