GEO series

The Transcription Factor TCF21 is Necessary for Adoption of Cell Fates by Foxd1+ Stromal Progenitors during Kidney Development

GSE325955 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2026/05/01 Platform GPL34290

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 14 samples: 12 distinct titles, 2 of them repeatedGroups 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.

Summary (written by the submitters)

The stromal compartment of the developing kidney arises from Foxd1-expressing progenitors and gives rise to diverse cell types essential for nephrogenesis, including the renal stroma, capsule, mesangial cells, renin cells, pericytes, and vascular smooth muscle cells (VSMCs). However, the molecular mechanisms guiding their fate specification remain incompletely defined.

Read the full summary ↓

Here, we identify the basic helix-loop-helix transcription factor Tcf21 as a critical determinant of stromal cell identity during kidney development. We performed single-cell RNA sequencing (scRNA-seq) on Foxd1-lineage cells isolated from embryonic day 14.5 (E14.5) Tcf21 conditional knockout (Tcf21-cKO) Foxd1Cre/+;Rosa26mTmG;Tcf21f/f and control kidneys, revealing seven transcriptionally distinct stromal subpopulations. Loss of Tcf21 resulted in marked depletion of Medullary/Perivascular stroma, Collecting duct associated stroma, Proliferating stroma, and Nephrogenic zone associated subpopulations, confirmed by immunostaining, which revealed severe constriction of medullary and collecting duct stromal spaces. Additionally, we identified a novel cluster unique to Tcf21-cKO kidneys, characterized by high expression of Endomucin (Emcn). These cells spanned pseudotime trajectories and were distributed broadly across the mutant kidney. These findings were corroborated by E14.5 single-cell ATAC sequencing (scATAC-seq), which confirmed altered chromatin accessibility in Tcf21-deficient stroma. To assess the persistence and downstream impact of these defects, we performed bulk and scRNA-seq at E18.5, revealing sustained expansion of Emcn+ cells with pro-fibrotic and perivascular transcriptional programs. Histological analyses at 2 months demonstrated lasting architectural disruption, interstitial fibrosis, and impaired renal function in Tcf21-cKO mice. Our results identify Tcf21 as a key regulator of stromal progenitor fate and establish a developmental origin for fibrotic remodeling and kidney dysfunction.

This dataset

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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 GSE325955_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1442706 and SRA study SRP686575. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 distinct titles, 2 of them repeated

E18.5_RNA_Control_Male ×2 E18.5_RNA_Mutant_Male ×2

Supports a case/control comparison: 7 samples read as cases, 7 as controls.

How we read this: Read from 14 sample titles: 12 distinct titles with little repetition. 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

GSM9617751 E14.5_scRNA_Control_Female
GSM9617752 E14.5_scRNA_Control_Male
GSM9617753 E14.5_scRNA_Mutant_Female
GSM9617754 E14.5_scRNA_Mutant_Male
GSM9617755 E18.5_scRNA_Control_Female
GSM9617756 E18.5_scRNA_Control_Male
GSM9617757 E18.5_scRNA_Mutant_Female
GSM9617758 E18.5_scRNA_Mutant_Male
GSM9617759 E14.5_scATAC_Control_Male
GSM9617760 E14.5_scATAC_Mutant_Male
GSM9617761 E18.5_RNA_Control_Male_1
GSM9617762 E18.5_RNA_Control_Male_2
GSM9617763 E18.5_RNA_Mutant_Male_1
GSM9617764 E18.5_RNA_Mutant_Male_2

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