Whole-genome bisulfite sequencing analysis for intestinal budding organoids derived from induced or tissue-derived intestinal stem cells, and for mouse embryonic fibroblasts

We have previously succeeded in generating induced fetal intestine-derived progenitor cells (iFIPCs) by expressing a gene set (Foxa3/Cdx2/Gata6/Hnf4a) in mouse embryonic fibroblasts (MEFs), which form spherical organoids (SOs) in three-dimensional culture, and subsequently maturated them into adult-type induced intestinal stem cells (iISCs), which form budding organoids (BOs) like tissue-derived intestinal stem cells (ISCs) (Miura & Suzuki, 2017). Although CpG methylation of genomic DNA is an essential epigenetic factor affecting the transcription during cell differentiation, little is known about how DNA methylation changes and what role it plays in the direct reprogramming. Therefore, we performed a genome-wide methylome analysis for iISC- and ISC-derived BOs (iISC-BO and ISC-BO, respectively) and MEFs. Overall design: We performed genome-wide and base-resolution methylome analysis using the post-bisulfite adaptor-tagging (PBAT) method (Miura et al., 2012) in MEFs, iISC-BOs, and ISC-BOs.