Protocol for investigating chromatin architecture in adult skeletal muscle stem cells using high-throughput chromosome conformation capture.

3D genome architecture is pivotal for gene transcription and cellular lineage development. However, it remains challenging to generate high-quality Hi-C (high-throughput chromosome conformation capture) libraries from rare cell populations. Here, we present a protocol for investigating chromatin architecture in adult skeletal muscle stem cells, also known as satellite cells (MuSCs), using Hi-C. We detail the procedures for isolating MuSCs, provide an in-depth guide for preparing Hi-C libraries, and introduce the use of the Microcket package for processing Hi-C data. For complete details on the use and execution of this protocol, please refer to Zhao et al.(1) and Zhao et al.(2).