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Series GSE250180 Query DataSets for GSE250180
Status Public on Apr 04, 2024
Title Extraembryonic gut endoderm cells undergo programmed cell death during development (RRBS)
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Despite a distinct developmental origin, extraembryonic cells in mice contribute to gut endoderm and converge to transcriptionally resemble their embryonic counterparts. Notably, extraembryonic progenitors share a non-canonical epigenome, raising several pertinent questions, including whether this landscape is reset to match the embryonic regulation and if these cells persist into later development. Here, we developed a two-color lineage tracing strategy to track and isolate extraembryonic cells over time. We find that extraembryonic gut cells display substantial memory of their developmental origin including retention of their original DNA methylation landscape and resulting transcriptional signatures. Furthermore, we show that extraembryonic gut cells undergo programmed cell death and neighboring embryonic cells clear their remnants via non-professional phagocytosis. By midgestation, we no longer detect extraembryonic cells in the wild type gut while they persist and differentiate further in p53 mutant embryos. Our study provides key insights into the molecular and developmental fate of extraembryonic cells inside the embryo.
 
Overall design DNA methylation profiling of sorted gut endoderm cells with embryonic and extraembryonic origin.
 
Contributor(s) Batki J, Hetzel S, Schifferl D, Bolondi A, Walther M, Wittler L, Grosswendt S, Herrmann BG, Meissner A
Citation(s) 38849542
Submission date Dec 14, 2023
Last update date Jul 01, 2024
Contact name Sara Hetzel
E-mail(s) hetzel@molgen.mpg.de
Organization name Max Planck Institute for Molecular Genetics
Department Genome Regulation
Lab Meissner Lab
Street address Ihnestraße 63
City Berlin
ZIP/Postal code 14195
Country Germany
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (32)
GSM7975135 RRBS_E135_emColon_EPCAM_GFP_WT_Rep1
GSM7975136 RRBS_E135_emColon_EPCAM_GFP_WT_Rep2
GSM7975137 RRBS_E135_emColon_EPCAM_GFP_WT_Rep3
This SubSeries is part of SuperSeries:
GSE250084 Extraembryonic gut endoderm cells undergo programmed cell death during development
Relations
BioProject PRJNA1052616

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Supplementary file Size Download File type/resource
GSE250180_RAW.tar 791.8 Mb (http)(custom) TAR (of BW)
GSE250180_RRBS_E135_emColon_EPCAM_GFP_WT_merged_mm10_10x.bw 34.5 Mb (ftp)(http) BW
GSE250180_RRBS_E135_emSI_EPCAM_GFP_WT_merged_mm10_10x.bw 34.6 Mb (ftp)(http) BW
GSE250180_RRBS_E135_exColon_EPCAM_mCherry_Trp53KO_merged_mm10_10x.bw 36.0 Mb (ftp)(http) BW
GSE250180_RRBS_E135_exSI_EPCAM_mCherry_Trp53KO_merged_mm10_10x.bw 16.4 Mb (ftp)(http) BW
GSE250180_RRBS_E95_YsEndo_mCherry_merged_mm10_10x.bw 50.6 Mb (ftp)(http) BW
GSE250180_RRBS_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_merged_mm10_10x.bw 48.0 Mb (ftp)(http) BW
GSE250180_RRBS_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_merged_mm10_10x.bw 44.4 Mb (ftp)(http) BW
GSE250180_RRBS_E95_exHindgut_EPCAM_mCherry_merged_mm10_10x.bw 55.2 Mb (ftp)(http) BW
GSE250180_RRBS_E95_exMidgut_EPCAM_mCherry_merged_mm10_10x.bw 45.3 Mb (ftp)(http) BW
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