High-content single-cell combinatorial indexing.

Animals Chromatin / genetics DNA / genetics Genome High-Throughput Nucleotide Sequencing / methods Humans Mice Sequence Analysis, DNA Single-Cell Analysis / methods Transposases / genetics

Journal

Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648

Informations de publication

Date de publication:
12 2021
Historique:
received: 08 01 2021
accepted: 20 05 2021
pubmed: 7 7 2021
medline: 15 4 2022
entrez: 6 7 2021
Statut: ppublish

Résumé

Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but produces sparse coverage in terms of usable reads per cell. We develop symmetrical strand sci ('s3'), a uracil-based adapter switching approach that improves the rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-assay for transposase-accessible chromatin, s3-ATAC) in human cortical and mouse whole-brain tissues, with mouse datasets demonstrating a six- to 13-fold improvement in usable reads per cell compared with other available methods. Application of s3 to single-cell whole-genome sequencing (s3-WGS) and to whole-genome plus chromatin conformation (s3-GCC) yields 148- and 14.8-fold improvements, respectively, in usable reads per cell compared with sci-DNA-sequencing and sci-HiC. We show that s3-WGS and s3-GCC resolve subclonal genomic alterations in patient-derived pancreatic cancer cell lines. We expect that the s3 platform will be compatible with other transposase-based techniques, including sci-MET or CUT&Tag.

Identifiants

DOI: 10.1038/s41587-021-00962-z PMID: 34226710 PMC: PMC8678206
pubmed: 34226710
doi: 10.1038/s41587-021-00962-z
pii: 10.1038/s41587-021-00962-z
pmc: PMC8678206
mid: NIHMS1707134
doi:

Substances chimiques

Chromatin 0
DNA 9007-49-2
Transposases EC 2.7.7.-

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

1574-1580

Subventions

Organisme : NCI NIH HHS
ID : R01 CA186241
Pays : United States
Organisme : NIDA NIH HHS
ID : R01 DA047237
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH113926
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM124704
Pays : United States

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

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Auteurs

Ryan M Mulqueen (RM)

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
ORCID: 0000-0002-3903-7594

Dmitry Pokholok (D)

Scale Bio, Berkeley, CA, USA.

Brendan L O'Connell (BL)

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
ORCID: 0000-0001-7757-4561

Casey A Thornton (CA)

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
ORCID: 0000-0003-3589-6911

Fan Zhang (F)

Scale Bio, Berkeley, CA, USA.

Brian J O'Roak (BJ)

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.

Jason Link (J)

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
Brendan Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA.

Galip Gürkan Yardımcı (GG)

Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA.

Rosalie C Sears (RC)

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
Brendan Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA.
Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA.
ORCID: 0000-0003-1558-2413

Frank J Steemers (FJ)

Scale Bio, Berkeley, CA, USA.

Andrew C Adey (AC)

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA. adey@ohsu.edu.
Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA. adey@ohsu.edu.
Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA. adey@ohsu.edu.
Department of Oncological Sciences, Oregon Health and Science University, Portland, OR, USA. adey@ohsu.edu.
Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA. adey@ohsu.edu.
ORCID: 0000-0001-7648-8717

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Techniques d'investigation › Techniques cytologiques › Analyse sur cellule unique › High-content single-cell combinatorial indexing.
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Transferases › Phosphotransferases › Nucleotidyltransferases › Transposases › High-content single-cell combinatorial indexing.