TY - JOUR
T1 - High-Throughput Single-Cell Sequencing with Linear Amplification
AU - Yin, Yi
AU - Jiang, Yue
AU - Lam, Kwan Wood Gabriel
AU - Berletch, Joel B.
AU - Disteche, Christine M.
AU - Noble, William S.
AU - Steemers, Frank J.
AU - Camerini-Otero, R. Daniel
AU - Adey, Andrew C.
AU - Shendure, Jay
N1 - Publisher Copyright:
© 2019 Elsevier Inc.
PY - 2019/11/21
Y1 - 2019/11/21
N2 - 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.
AB - 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.
KW - DNA repair
KW - chromosome segregation
KW - double-strand break
KW - homologous recombination
KW - infertility
KW - linear amplification
KW - meiotic crossover
KW - mouse
KW - single-cell combinatorial indexing
KW - single-cell sequencing
UR - http://www.scopus.com/inward/record.url?scp=85074992710&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85074992710&partnerID=8YFLogxK
U2 - 10.1016/j.molcel.2019.08.002
DO - 10.1016/j.molcel.2019.08.002
M3 - Article
C2 - 31495564
AN - SCOPUS:85074992710
SN - 1097-2765
VL - 76
SP - 676-690.e10
JO - Molecular Cell
JF - Molecular Cell
IS - 4
ER -