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Extraembryonic gut endoderm cells undergo programmed cell death during development (RNA-seq)

GSE250083 Mus musculus (mouse) RNA-seq (gene expression) 44 samples Submitted 2024/04/04 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 44 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
44 samples: 12 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Extraembryonic gut endoderm cells undergo programmed cell death during developmentNature cell biology · 2024
Summary (written by the submitters)
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.
Read the full summary ↓
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.
Published in
Extraembryonic gut endoderm cells undergo programmed cell death during development
Batki J, Hetzel S, Schifferl D et al. · Nature cell biology 2024 · PMID 38849542 · doi:10.1038/s41556-024-01431-w
This dataset
Open GSE250083 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE250083_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1052002 and SRA study SRP477791. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38849542) ↗
Study design
12 conditions, mostly with about 4 replicates each
RNAseq_E65_Epi_GFP ×4 RNAseq_E65_exEndo1_mCherry ×4 RNAseq_E65_exEndo2_mCherry ×4 RNAseq_E95_YsEndo_mCherry ×4 RNAseq_E95_emHindgut_EPCAM_GFP_mCherry_dual_l… ×4 RNAseq_E95_emMidgut_EPCAM_GFP_mCherry_dual_low ×4 RNAseq_E95_exHindgut_EPCAM_mCherry ×4 RNAseq_E95_exMidgut_EPCAM_mCherry ×4 +4 more

Supports a between-group comparison across 44 samples.

How we read this: 12 replicated groups read from 44 sample titles; they account for 44 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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