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Systematic benchmarking of single-cell ATAC sequencing protocols

ABSTRACT: We systematically benchmarked 8 single-cell ATAC sequencing technologies for their capacity to generate high-quality single-cell open chromatin profiles, and to elucidate the regulatory landscape of complex samples. Our study contains 47 individual human PBMC scATAC-seq experiments from a reference male and female donor. To streamline data analysis, we devised PUMATAC (https://github.com/aertslab/PUMATAC), a flexible and universal data analysis pipeline and best practices repository for scATAC-seq. Systematic technology-specific differences in sequencing library complexity and biases in tagmentation specificity were found to impact the accuracy of cell type annotation, genotype demultiplexing, peak calling, differential region accessibility, and motif enrichment. Together, our data forms a new scATAC-seq reference of more than 169, 000 PBMC cells with matched single-cell multiome and RNA-seq data.

ORGANISM(S): Homo sapiens

PROVIDER: GSE194028 | GEO | 2023/05/22

REPOSITORIES: GEO

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