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

Zhang, Xuan; Marand, Alexandre P.; Yan, Haidong; Schmitz, Robert J. (ORCID:0000000175386663)

doi:10.1186/s13059-024-03235-5

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

Zhang, Xuan·Marand, Alexandre P.·Yan, Haidong·Schmitz, Robert J. (ORCID:0000000175386663)

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Abstract

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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59 BASIC BIOLOGICAL SCIENCES ATAC-seq chromatin accessibility combinatorial fluidic indexing massive-scale single-cell

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BibTeX RIS

Zhang, Xuan, Marand, Alexandre P., Yan, Haidong, Schmitz, Robert J. (ORCID:0000000175386663). 2024-04-08. scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. https://doi.org/10.1186/s13059-024-03235-5

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