Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing.

ABSTRACT: Here we present advancements in single-cell combinatorial indexed Assay for Transposase Accessible Chromatin (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve atlas-scale cell throughput (>10⁵ cells) at low cost. The platform leverages the core of the sciATAC workflow where multiple indexed tagmentation reactions are performed, followed by pooling and distribution to a second set of reaction wells for polymerase chain reaction (PCR)-based indexing. In this work, we instead leverage a chip containing 5184 nanowells at the PCR stage of indexing, enabling a 52-fold improvement in scale and reduction in per-cell preparation costs. We detail three variants that balance cell throughput and depth of coverage, and apply these methods to banked mouse br

SUBMITTER: O'Connell BL 

PROVIDER: S-EPMC10069466 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature