Purification of GFP-tagged nuclei from frozen livers of INTACT mice for RNA- and ATAC-sequencing

Summary Isolation of nuclei tagged in specific cell types (INTACT) allows for stress-free and high-throughput analyses of cellular subpopulations. Here, we present an improved protocol for isolation of pure and high-quality GFP-labeled nuclei from frozen livers of INTACT mice, as well as protocols for downstream sequencing analyses. The adaptation to frozen tissue provides a pause point that allows sampling at multiple time points and/or phenotypic characterization of livers prior to nuclei isolation and downstream analyses. For complete details on the use of this protocol, please refer to Loft et al. (2021).
Graphical abstract
Highlights • Optimized protocol for isolation of nuclei from frozen livers • Protocol for immunopurification of nuclei tagged in specific cell types (INTACT) • Preparation of nuclear RNA- and ATAC-seq libraries • Nuclei from frozen and fresh livers perform equally in downstream assays
Isolation of nuclei tagged in specific cell types (INTACT) allows for stress-free and high-throughput analyses of cellular subpopulations. Here, we present an improved protocol for isolation of pure and high-quality GFP-labeled nuclei from frozen livers of INTACT mice, as well as protocols for downstream sequencing analyses. The adaptation to frozen tissue provides a pause point that allows sampling at multiple time points and/or phenotypic characterization of livers prior to nuclei isolation and downstream analyses.