Gene expression data from human iPSC differentiated to macrophages and microglia, compared to human blood-derived monocytes and human primary fetal microglia

A human Pluripotent Stem Cell microglia model displays a neuronal-co-culture-specific expression profile and inflammatory response Walther Haenseler, Stephen N. Sansom, Julian Buchrieser, Sarah E. Newey, Craig S. Moore, Francesca J. Nicholls, Satyan Chintawar, Christian Schnell, Jack P. Antel, Nicholas D. Allen, M. Zameel Cader, Richard Wade-Martins, William S. James, Sally A. Cowley The aim of the experiment was to compare the gene expression profiles from human iPSC-derived embryonic macrophages (both precursors, mature, and cells cultured in 'microglia medium'), with iPSC-macrophages differentiated to microglia by co-culture with iPSC-derived cortical neurons. They were also compared to human blood-derived monocytes and to human primary fetal microglia. 1 replicate of each of 3 genetic backgrounds for each condition were used. bloodMono were extracted from PBMCs with CD14 MACS beads. iMono were iPSC-derived macrophage precursors, from 3 control lines. iMac were from the same harvest as iMono - cells were set up in macrophage differentiation medium for 2 weeks; iMGL were as per iMac but cultured in microglia medium; co-iMG (AKA iMG) were as per iMGL but added to SBAD3-01 iPSC-derived cortical neurons, after 2 wks dissociated with accutase and co-iMG were selected with CD11b MACS beads. See manuscript for full cell culture details. RNA was extracted using an RNeasy kit (Qiagen) for Illumina HT12v4 transcriptome array analysis. fetalMG were human fetal microglia samples (at pre-myelinating gestational ages of fetalMG_1 20, fetalMG_2 23, fetalMG_3 15 weeks) cultured ex vivo in DMEM supplemented with 5% FBS for 5-7 days prior to RNA isolation using standard TrizolTM methods.