High-Throughput Single-Cell Sequencing with Linear Amplification

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2019 Sep 10

PMID 31495564

Citations 49

Authors

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

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.

Chovanec P, Yin Y Nucleic Acids Res. 2025; 53(4).

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Scalable co-sequencing of RNA and DNA from individual nuclei.

Olsen T, Talla P, Sagatelian R, Furnari J, Bruce J, Canoll P Nat Methods. 2025; 22(3):477-487.

PMID: 39939719 DOI: 10.1038/s41592-024-02579-x.

Advances and applications in single-cell and spatial genomics.

Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X Sci China Life Sci. 2025; .

PMID: 39792333 DOI: 10.1007/s11427-024-2770-x.

HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling.

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