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Series GSE222669 Query DataSets for GSE222669
Status Public on Dec 19, 2023
Title Whole-genome bisulfite sequencing analysis for intestinal budding organoids derived from induced or tissue-derived intestinal stem cells, and for mouse embryonic fibroblasts
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary 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.
 
Contributor(s) Horisawa K, Miura S, Araki H, Miura F, Ito T, Suzuki A
Citation(s) 38102164
Submission date Jan 11, 2023
Last update date Dec 20, 2023
Contact name Atsushi Suzuki
Organization name Kyushu University
Department Medical Institute of Bioregulation
Lab Division of Organogenesis and Regeneration
Street address 3-1-1 Maidashi, Higashi-ku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8582
Country Japan
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (8)
GSM6928645 PBAT sample for MEF, replicate 1
GSM6928646 PBAT sample for MEF, replicate 2
GSM6928647 PBAT sample for MEF, replicate 3
Relations
BioProject PRJNA922997

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE222669_RAW.tar 36.0 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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