title: GSM5914838: Cerebral cortex, dMCAO, d14, rep3; Mus musculus; RNA-Seq
library_construction_protocol: [Nuclei isolation from frozen samples]  Frozen mouse brain tissue samples were homogenized and lysed with Triton X-100 in RNase-free water for nuclei isolation. The isolated nuclei were purified, centrifuged, and resuspended in PBS with BSA and RNAse Inhibitor. The nuclei were diluted to 700 nuclei/ul and loaded to 10x Genomics Chromium Controller to encapsulate single nuclei into droplet emulsions following the manufacturer's recommendations (Pleasanton, CA, United States). Library preparation was performed according to the instructions in the Chromium Next GEM 3' Single Cell Reagent kits v3.1. Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA). Libraries were sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA, United States), and reads were subsequently processed using 10x Genomics Cell Ranger analytical pipeline (v4.0) and mouse mm10 pre-mRNA reference. Dataset aggregation was performed using the cellranger aggr function normalizing for the total number of confidently mapped reads across libraries.