Purification of mouse hepatic non-parenchymal cells or nuclei for use in ChIP-seq and other next-generation sequencing approaches

Significant advancements in understanding disease mechanisms can occur through combined analysis of next-generation sequencing datasets generated using purified cell populations. Here, we detail our optimized protocol for purification of mouse hepatic macrophages (or other liver non-parenchymal populations) suitable for use in various next-generation sequencing protocols. An alternative framework is described for sorting pre-fixed hepatic nuclei populations. This strategy has the advantage of rapidly preserving the nuclei and can facilitate success with ChIP-seq for more challenging molecules.For complete details on the use and execution of these protocols, please refer to Muse et al. (2018), Sakai et al. (2019), and Seidman et al. (2020).

Automated summary

Significant advancements in understanding disease mechanisms can be achieved through combined analysis of next-generation sequencing datasets from purified cell populations. This article details an optimized protocol for purifying mouse hepatic macrophages and an alternative framework for sorting pre-fixed hepatic nuclei populations. This strategy offers the advantage of rapidly preserving nuclei and facilitating success with ChIP-seq for more challenging molecules.