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A Standardized Protocol for Generating iPSC-Derived Human Microglia for Functional Genomic Assays.

Jason Ngo·Emily Lee·Marta Olah·Falak Sher
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Abstract

Human induced pluripotent stem cell (iPSC)-derived microglia (iMG) provide an in vitro experimental system for studying human microglial biology, neuroinflammation, and genetic risk mechanisms associated with neurological disease. This chapter describes a standardized, scalable, and reproducible protocol for the differentiation of human iPSCs into functional microglia-like cells, with particular emphasis on applications in transcriptional and epigenomic network analysis. The protocol supports high-viability floating iMG production, compatibility with pooled CRISPR perturbation approaches, and downstream multiomic profiling, including single-cell RNA sequencing, chromatin accessibility assays, and proteomics. Detailed procedures are provided for iPSC maintenance, hematopoietic progenitor cell generation, microglial maturation, functional genomics integration, and quality control.

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HumansInduced Pluripotent Stem CellsMicrogliaCell DifferentiationGenomicsCell Culture TechniquesSingle-Cell Gene Expression AnalysisCells, CulturedEpigenomicsATAC-seqCRISPR screeningFunctional genomicsPerturb-seqSingle-cell RNA sequencingStem cell differentiationTranscriptional networksiPSC-derived microgliaJournal Article

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Jason Ngo, Emily Lee, Marta Olah, Falak Sher. 2027. A Standardized Protocol for Generating iPSC-Derived Human Microglia for Functional Genomic Assays.. https://doi.org/10.1007/978-1-0716-5539-9_6

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