Fluorescence-activated nuclei sorting (FANS) of purified neural cell populations from mouse cortex for multi-omic profiling v2

Increased understanding of the functional complexity of the genome has led to growing recognition about the role of epigenetic/transcriptional variation in health and disease. Because epigenetic processes play a critical role in determining cell type-specific patterns of gene regulation it is important to consider cellular composition in regulatory genomic studies of heterogeneous tissue like the brain. Building on a previous protocol for isolating purified populations of nuclei from different cortical cell types from human post-mortem brain tissue, this protocol uses fluorescence-activated nuclei sorting (FANS) to isolate and profile nuclei from multiple different cell types from frozen mouse cortex. This protocol can be used to robustly purify populations of neuronal (NeuN+ve) and microglia (PU.1+ve) and other glial origin nuclei (NeuN-ve/PU.1-ve) from frozen mouse cortex tissue, with each sample yielding purified populations of nuclei amenable to simultaneous analysis of i) DNA modifications (via bisulfite sequencing/microarray), ii) histone modifications, iii) chromatin accessibility (via ATAC-seq), and iv) gene expression (via RNA-seq).