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The absence of Trim28 in nephron progenitors results in impaired kidney development and function

GSE327974 Mus musculus (mouse) Single-cell RNA-seq 8 samples Submitted 2026/08/02 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 8 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
8 samples: 3 × Bulk RNA_seq KO_kidney_biol vs 3 × Bulk RNA_seq Cntrl_kidney_biolGroups 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 TRIM28 gene encodes a transcriptional regulator involved in a variety of molecular processes. Inactivation of TRIM28 has been linked to the epithelial subtype of Wilms tumor, the most common paediatric renal malignancy. Therefore, TRIM28 may also impact early kidney morphogenesis. To investigate its role in nephrogenesis, we analyzed Trim28 conditional knockout (Trim28Δ/Δ) mice.
Read the full summary ↓
We found that deleting Trim28 in nephron progenitors resulted in early postnatal lethality and reduced kidney weight. While all renal structures were present, the proximal tubules (PTs) were disorganized. Transcriptome analyses revealed cell-type-specific deregulation of retroelement expression following Trim28 deletion. Further analysis of scRNA-seq data revealed a decreased frequency of nephron progenitor cells (NPCs), an increase in PT cells, and a clear shift towards inflammatory gene expression patterns. While there was no evidence of tumor formation in Trim28Δ/Δ kidneys, the differentially expressed genes in Trim28Δ/Δ progenitors reflected reduced translation, similar to patterns observed in TRIM28 mutant tumor-derived NPCs. Thus, our data demonstrate that TRIM28 primarily influences the maintenance and differentiation of NPCs and PT cells, as well as their subsequent function.
This dataset
Open GSE327974 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 GSE327974_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1453426 and SRA study SRP691732. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × Bulk RNA_seq KO_kidney_biol vs 3 × Bulk RNA_seq Cntrl_kidney_biol

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 8 sample titles; they account for 6 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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