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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 676-690.e10 |
| Journal | Molecular Cell |
| Volume | 76 |
| Issue number | 4 |
| DOIs | |
| State | Published - Nov 21 2019 |
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Keywords
- 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
Cite this
High-Throughput Single-Cell Sequencing with Linear Amplification. / Yin, Yi; Jiang, Yue; Lam, Kwan Wood Gabriel; Berletch, Joel B.; Disteche, Christine M.; Noble, William S.; Steemers, Frank J.; Camerini-Otero, R. Daniel; Adey, Andrew C.; Shendure, Jay.
In: Molecular Cell, Vol. 76, No. 4, 21.11.2019, p. 676-690.e10.Research output: Contribution to journal › Article
}
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
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 - chromosome segregation
KW - DNA repair
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
VL - 76
SP - 676-690.e10
JO - Molecular Cell
JF - Molecular Cell
SN - 1097-2765
IS - 4
ER -