scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing

Zhang, Xuan; Marand, Alexandre P.; Yan, Haidong; Schmitz, Robert J.

doi:10.1186/s13059-024-03235-5

Title: scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing

Journal Article · 07 April 2024 · Genome Biology (Online)

DOI: https://doi.org/10.1186/s13059-024-03235-5 · OSTI ID:2335532

Zhang, Xuan; Marand, Alexandre P.; Yan, Haidong;

Abstract Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present a novel technique called scifi-ATAC-seq, single-cell combinatorial fluidic indexing ATAC-sequencing, which combines a barcoded Tn5 pre-indexing step with droplet-based single-cell ATAC-seq using the 10X Genomics platform. With scifi-ATAC-seq, up to 200,000 nuclei across multiple samples can be indexed in a single emulsion reaction, representing an approximately 20-fold increase in throughput compared to the standard 10X Genomics workflow.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0023338

OSTI ID:: 2335532

Alternate ID(s):: OSTI ID: 2345727

Journal Information:: Genome Biology (Online), Journal Name: Genome Biology (Online) Journal Issue: 1 Vol. 25; ISSN 1474-760X

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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