snRNA-seq of mus musculus: adult male amydala BL6
After microdissection of amygdala tissue, single nuclei suspension and library generation followed the 10X protocol for the Chromium Next GEM Automated Single Cell 3 Library and Gel Bead Kit v3.1 (cat# PN-100014) as described except for the following modifications: Nuclei suspension were generated using the recommended method from the 10X scMultiome protocol (CG000375 Rev C) to lyse cells and obtain nuclei; however, we skipped the nuclei permeabilization step after sorting. Following single nuclei suspension generation, nuclei were counterstained for 7-AAD and NeuN-405 antibody (Novus Biologicals, 1:200) and sorted on a MACSQuant Tyto prior to GEM generation. We selected for a 75-25 split of NeuN+/7-AAD+ nuclei for neurons and NeuN-/7-AAD+ for non-neuronal nuclei respectively. We captured ~10,000 nuclei per genotype per region per replicate on a single 10X GEM chip. All downstream library preparation was done according to the 10X protocol (CG000286) and sequenced on a Novaseq 6000 with a target of ~40-50k reads per nucleus.