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SETD3 regulates endoderm differentiation of mouse embryonic stem cells through its effect on the canonical Wnt signaling pathway activity

GSE242033 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/03/13 Platform GPL13112
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathwayFASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024
Summary (written by the submitters)
With self-renewal and pluripotency features, embryonic stem cells (ESCs) provide an invaluable tool to investigate early cell fate decisions. Pluripotency exit and lineage commitment depend on precise regulation of gene expression that requires coordination between transcription (TF) and chromatin factors in response to various signaling pathways.
Read the full summary ↓
SET domain-containing 3 (SETD3) is a methyltransferase that can modify histones in the nucleus and actin in the cytoplasm. Through an shRNA screen, we previously identified SETD3 as an important factor in meso/endodermal lineage commitment of mouse ESCs (mESC). In this study, we identified SETD3-dependent transcriptomic changes during endoderm differentiation of (mESCs) using time-course RNA-seq analysis. We found that SETD3 is involved in timely activation of the endoderm-related gene network. Canonical Wnt signaling pathway was one of the markedly altered signaling pathways in the absence of SETD3. The assessment of Wnt transcriptional activity revealed a significant reduction in setd3∆ mESCs coincident with a decrease in nuclear pool of the key TF β-catenin level, though no change was observed in its mRNA or total protein level. Furthermore, proximity ligation assay found an interaction between SETD3 and β-catenin. We were able to rescue the differentiation defect by stably re-expressing SETD3 or activating the canonical Wnt signaling pathway by changing mESC culture conditions. Our results suggest that alterations in canonical Wnt pathway activity and subcellular localization of β-catenin might contribute to the endoderm differentiation defect of setd3∆ mESCs.
Published in
SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathway
Alganatay C, Balbasi E, Tuncbag N et al. · FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2024 · PMID 38334393 · doi:10.1096/fj.202301883R
This dataset
Open GSE242033 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 GSE242033_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 PRJNA1011246 and SRA study SRP457770. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38334393) ↗
Study design
8 conditions, mostly in triplicate
setd3Δ cells, endoderm differentiation, Day 0, ×3 setd3Δ cells, endoderm differentiation, Day 2, ×3 setd3Δ cells, endoderm differentiation, Day 3, ×3 setd3Δ cells, endoderm differentiation, Day 4, ×3 CJ9 cells, endoderm differentiation, Day 0, ×3 CJ9 cells, endoderm differentiation, Day 2, ×3 CJ9 cells, endoderm differentiation, Day 3, ×3 CJ9 cells, endoderm differentiation, Day 4, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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