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Updated: Sep 24, 2025
Chromatin Immunoprecipitation from Human Embryonic Stem Cells
Published on: July 22, 2008
Chromatin Immunoprecipitation in Human Pluripotent Stem Cell-Derived 3D Organoids to Analyze DNA-Protein Interactions
Wei Xuan Tan1,2, Chek Mei Bok1, Natasha Hui Jin Ng1
1Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
Abstract:
Chromatin immunoprecipitation (ChIP) is a technique that has been widely used to interrogate DNA-protein interactions in cells. In recent years, human pluripotent stem cell (hPSC)-derived 3D organoids have emerged as a powerful model to understand human development and diseases. Performing ChIP in hPSC-derived 3D organoids is a useful approach to dissect the roles of transcription factors or co-factors and to understand the epigenetic landscape in human development and diseases. However, performing ChIP in 3D organoids is more challenging than monolayer cultures, and an optimized protocol is needed for interpretable data. Hence, in this chapter, we describe in detail a protocol for performing ChIP in hPSC-derived islet-like cells as an example, from organoid harvest to ChIP-qPCR data analysis. This chapter also highlights potential pitfalls and provides recommendations for troubleshooting.
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