scifi-ATAC-seq：基于组合式流体索引的大规模单细胞染色质可及性测序

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

机构信息

Department of Genetics, University of Georgia, Athens, GA, USA.

Current address: Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA.

出版信息

Genome Biol. 2024 Apr 8;25(1):90. doi: 10.1186/s13059-024-03235-5.

DOI:10.1186/s13059-024-03235-5

PMID:38589969

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11003106/

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.

摘要

单细胞 ATAC-seq 技术的出现，为在细胞类型特异性水平上全面揭示候选顺式调控元件提供了一种强大的方法。然而，目前的单细胞方法存在通量有限和成本高的问题。在这里，我们提出了一种名为 scifi-ATAC-seq 的新技术，即单细胞组合式流体索引 ATAC 测序，它将带有条形码的 Tn5 预索引步骤与基于液滴的单细胞 ATAC-seq 相结合，使用 10X Genomics 平台进行操作。通过 scifi-ATAC-seq，在单个乳液反应中可以对多达 200,000 个核进行索引，与标准的 10X Genomics 工作流程相比，通量提高了约 20 倍。