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Nat Commun. 2018 Dec 17;9(1):5345. doi: 10.1038/s41467-018-07771-0.

A rapid and robust method for single cell chromatin accessibility profiling.

Author information

1
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
2
MedImmune, Sir Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, UK.
3
Functional Biology and Metabolism Unit, Biochemistry and Molecular Biology, SDU, 5230, Odense, Denmark.
4
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. st9@sanger.ac.uk.
5
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. st9@sanger.ac.uk.
6
Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge, CB3 0HE, UK. st9@sanger.ac.uk.

Abstract

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, very few studies have been performed at the single cell level (scATAC-seq) due to technical challenges. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk Tn5 tagging with single-nuclei sorting. We demonstrate that our method works robustly across various systems, including fresh and cryopreserved cells from primary tissues. By profiling over 3000 splenocytes, we identify distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors.

PMID:
30559361
PMCID:
PMC6297232
DOI:
10.1038/s41467-018-07771-0
[Indexed for MEDLINE]
Free PMC Article

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