Gene expression profiles of human iPSC-derived microglia in different culture conditions [Bulk RNAseq]

iPSC-derived microglia precursor cells were integrated into the cerebral organoid slice cultures, FACS sorted based on expression of green fluorescent protein after 10 and 60 days, and compared to iPSC-derived microglia in monoculture. The expression profiles were further compared to published RNAseq data from primary human microglia and iPSC-derived human microglia transplanted in the mouse brains. Overall design: Microglial precursor cells were cultured as monocultures or added to cerebral organoid slice cultures. For bulk RNA sequencing, the cells were FACS sorted based on their green fluorescent protein expression. The samples originated from different batches of differentiations from an iPSC line obtained from human foreskin fibroblasts from a healthy 2-year-old male from the Coriell Institute (AG07095) and from an already established and characterized embryonic stem cell line H1. From the iPSC line, microglia precursor cells were analyzed, microglia in monoculture (after 10 and 60 days), and microglia in cerebral organoids (after 10 and 60 days). In addition, microglia in cerebral organoids were treated with levetiracetam or PBS-control and analyzed. From the H1 line, microglia cultured for 60 days in cerebral organoid slice cultures were analyzed. An n=6 was used for each sample set, except for microglia in cerebral organoid slice cultures treated with levetiracetam (n=2) and treated with PBS-control (n=3). One n corresponds to all collected GFP+ cells pooled from 4-6 organoid sections for cells isolated from organoid sections. For microglia monoculture and microglia precursor samples, one n corresponds to two pooled wells of a 6-well plate, with one plate generating three samples. The microglia precursor cells were floating cells.