title: GSM8541708: Cortex, XPro1595 CPZ3, rep2; Mus musculus; RNA-Seq
library_construction_protocol: Brain cortex tissue was suspended in 500 µL homogenization buffer (Nuclei Isolation Kit, Sigma-Aldrich, NUC201) and homogenised in a pre-cooled 2 mL dounce homogeniser. The homogenate was filtered through a cell strainer cap (70μM) and centrifuged at 600g for 5 min. Thereafter, nuclei were subjected to an additional clean-up step by resuspending in freshly prepared nuclei wash buffer and density centrifugation for the gradient of the layered nuclei/29% iodixanol solution at 5000g for 15 mins at 4 °C. Nuclei pellets were collected. SnRNA-Seq performed in samples processed as per 10× Genomics Chromium Single Cell Reagent Kits Protocol (chemistry: Single Cell 3′ v2). The samples were processed to target 10,000 nuclei per sample. SnRNA-Seq was performed according to the manufacturers instructions (10× Genomics Chromium Single Cell 3' v3). The samples were processed to target 10,000 nuclei per sample. Briefly, 12 cycles of cDNA amplification were performed, and 12 cycles of final indexing PCR. cDNA concentrations were measured using Qubit dsDNA HS Assay Kit (ThermoFisher, Q32851). cDNA and library preparations were assessed using the Bioanalyzer High-Sensitivity DNA Kit. All samples were pooled to equimolar concentration and sequenced together on an Illumina NovaSeq 6000.