The brain and spinal cord were perfused with ice-cold HBSS and tissue was digested using the Neural Tissue Dissociation Kit from Miltenyi Biotec. Cells were washed twice in HBSS and myelin was removed by negative selection using myelin removal beads (Miltenyi Biotec, 130-096-433). For RNA-Seq experiments, cells were then incubated with microglia antibodies CD11b and CD45 for 20 minutes at 4°C in the dark and then flow-sorted on an LSR-Fortessa (BD Biosciences). DAPI (Cambridge Bioscience) was used to exclude dead cells. For all other experiments, microglia were isolated after myelin removal by positive section using CD11b beads (Miltenyi Biotec, 130-093-634).

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