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Series GSE221362 Query DataSets for GSE221362
Status Public on Apr 04, 2024
Title Extraembryonic gut endoderm cells undergo programmed cell death during development (scRNA-seq)
Organism Mus musculus
Experiment type Expression 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 Single-cell RNA-seq 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
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Submission date Dec 19, 2022
Last update date May 15, 2024
Contact name Sara Hetzel
Organization name Max Planck Institute for Molecular Genetics
Department Genome Regulation
Lab Meissner Lab
Street address Ihnestra├če 63
City Berlin
ZIP/Postal code 14195
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (3)
GSM6859078 scRNA_E95_mCherry_and_GFP_mCherry_dual
GSM7975176 scRNA_E135_gastrointestinal_tract_EPCAM_WT
GSM7975177 scRNA_E135_gastrointestinal_tract_EPCAM_Trp53KO
This SubSeries is part of SuperSeries:
GSE250084 Extraembryonic gut endoderm cells undergo programmed cell death during development
BioProject PRJNA913958

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Supplementary file Size Download File type/resource
GSE221362_RAW.tar 482.1 Mb (http)(custom) TAR (of TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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