title: GSM7882871: WT_Microglia_mouse1; Mus musculus; RNA-Seq
library_construction_protocol: After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina).