Complete mtesr plus

Human induced pluripotent stem cells (iPSCs) were maintained on Matrigel (BD Biosciences) in complete mTeSR Plus (STEMCELL Technologies, 100–0276). iPSCs were passaged every 5–6 days using ReLeSR dissociation reagent (STEMCELL Technologies, 05872) and used for hematopoietic stem cell differentiation with STEMdiff Hematopoietic kit (STEMCELL Technologies, 05310) followed by differentiation to induced microglial-like cells (iMGLs) using a previously published protocol [53 (link)]. iPSC lines were confirmed to have a normal karyotype (KaryoStat assay, Thermo Fisher Scientific). iMGLs were maintained and fed with a microglial medium supplemented with three factors (100ng/ml IL34, 50ng/ml TGFβ, 25ng/ml MCSF) for 25 days. On day 25, iMGLs were additionally supplemented with two factors (CX3CL1 and CD200, 100ng/ml each) for an additional three days. Mature iMGLs (day 28) were used for bulk RNA-seq analyses and functional assays.

Human induced pluripotent stem cells (iPSCs) were maintained on Matrigel (BD Biosciences) in complete mTeSR Plus (STEMCELL Technologies, 100-0276). iPSCs were passaged every 5–6 days using ReLeSR dissociation reagent (STEMCELL Technologies, 05872) and used for hematopoietic stem cell differentiation with STEMdiff Hematopoietic kit (STEMCELL Technologies, 05310) followed by differentiation to induced microglial-like cells (iMGLs) using a previously published protocol^{52 (link)}. An example of mature iMGLs culture and the expression level of known transcription factors and microglial markers is shown in Supplementary Fig. 8. iPSC lines were confirmed to have a normal karyotype (KaryoStat assay, Thermo Fisher Scientific). iMGLs were maintained and fed with a microglial medium supplemented with three factors (100 ng/ml IL34, 50 ng/ml TGFβ, 25 ng/ml MCSF) for 25 days. On day 25, iMGLs were additionally supplemented with two factors (CX3CL1 and CD200, 100 ng/ml each) for an additional three days. Mature iMGLs (day 28) were used for bulk RNA-seq analyses and functional assays.