High-Throughput Single-Cell Sequencing with Linear Amplification

Yi Yin, Yue Jiang, Kwan Wood Gabriel Lam, Joel B. Berletch, Christine M. Disteche, William S. Noble, Frank J. Steemers, R. Daniel Camerini-Otero, Andrew C. Adey, Jay Shendure

Research output: Contribution to journalArticle

5 Scopus citations


Conventional methods for single-cell genome sequencing are limited with respect to uniformity and throughput. Here, we describe sci-L3, a single-cell sequencing method that combines combinatorial indexing (sci-) and linear (L) amplification. The sci-L3 method adopts a 3-level (3) indexing scheme that minimizes amplification biases while enabling exponential gains in throughput. We demonstrate the generalizability of sci-L3 with proof-of-concept demonstrations of single-cell whole-genome sequencing (sci-L3-WGS), targeted sequencing (sci-L3-target-seq), and a co-assay of the genome and transcriptome (sci-L3-RNA/DNA). We apply sci-L3-WGS to profile the genomes of >10,000 sperm and sperm precursors from F1 hybrid mice, mapping 86,786 crossovers and characterizing rare chromosome mis-segregation events in meiosis, including instances of whole-genome equational chromosome segregation. We anticipate that sci-L3 assays can be applied to fully characterize recombination landscapes, to couple CRISPR perturbations and measurements of genome stability, and to other goals requiring high-throughput, high-coverage single-cell sequencing.

Original languageEnglish (US)
Pages (from-to)676-690.e10
JournalMolecular Cell
Issue number4
StatePublished - Nov 21 2019


  • chromosome segregation
  • DNA repair
  • double-strand break
  • homologous recombination
  • infertility
  • linear amplification
  • meiotic crossover
  • mouse
  • single-cell combinatorial indexing
  • single-cell sequencing

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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  • Cite this

    Yin, Y., Jiang, Y., Lam, K. W. G., Berletch, J. B., Disteche, C. M., Noble, W. S., Steemers, F. J., Camerini-Otero, R. D., Adey, A. C., & Shendure, J. (2019). High-Throughput Single-Cell Sequencing with Linear Amplification. Molecular Cell, 76(4), 676-690.e10. https://doi.org/10.1016/j.molcel.2019.08.002