RNAseq of mus musculus: adult brain and blood
To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately.  RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78.