Profiling chromatin accessibility at the single-cell level provides critical information about cell type composition and cell-to-cell variation within a complex tissue. Emerging techniques for the interrogation of chromatin accessibility in individual cells allow investigation of the fundamental mechanisms that lead to the variability of different cells. This protocol describes a fast and robust method for single-cell chromatin accessibility profiling based on the assay for transposase-accessible chromatin using sequencing (ATAC-seq). The method combines up-front bulk Tn5 tagging of chromatin with flow cytometry to isolate single nuclei or cells. Reagents required to generate sequencing libraries are added to the same well in the plate where cells are sorted. The protocol described here generates data of high complexity and excellent signal-to-noise ratio and can be combined with index sorting for in-depth characterization of cell types. The whole experimental procedure can be finished within 1 or 2 d with a throughput of hundreds to thousands of nuclei, and the data can be processed by the provided computational pipeline. The execution of the protocol only requires basic techniques and equipment in a molecular biology laboratory with flow cytometry support.

在单细胞水平上分析染色质可及性提供了有关复杂组织内细胞类型组成和细胞间变异的关键信息。用于询问单个细胞中染色质可及性的新兴技术允许研究导致不同细胞变异的基本机制。该协议描述了一种基于使用测序（ATAC-seq）对转座酶可访问染色质进行测定的单细胞染色质可访问性分析的快速而可靠的方法。该方法将染色质的前期批量 Tn5 标记与流式细胞术相结合，以分离单核或细胞。生成测序文库所需的试剂被添加到板中细胞被分类的同一个孔中。此处描述的协议生成高复杂性和出色信噪比的数据，并且可以与索引排序相结合，以深入表征细胞类型。整个实验过程可以在 1 或 2 天内完成，吞吐量为数百至数千个核，数据可以通过提供的计算管道进行处理。该协议的执行只需要在具有流式细胞仪支持的分子生物学实验室中使用基本技术和设备。