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Biomimetic fractal topography enhances podocyte maturation in vitro

GSE298416 Mus musculus (mouse) Single-cell RNA-seq 17 samples Submitted 2025/09/29 Platform GPL34290
At a glance

Single-cell RNA-seq · mouse · 17 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
17 samples: 6 × E11 murine podocytes, RT, vs 6 × E11 murine podocytes, HF, vs 5 × E11 murine podocytes, NT,Groups 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
Biomimetic fractal topography enhances podocyte maturation in vitroNature communications · 2025
Summary (written by the submitters)
Cells and tissues in their native environment are organized into intricate fractal structures, which are rarely recapitulated in their culture in vitro. The extent to which fractal patterns that resemble complex topography in vivo influence cell maturation, and the cellular responses to such shape stimulation remain inadequately elucidated.
Read the full summary ↓
Yet, the application of fractal cues (topographical stimulation via self-similar patterns) as an external input may offer a much-needed solution to the challenge of improving the differentiated cell phenotype in vitro. Here, we established fractality in the kidney glomerulus and podocytes, branching highly differentiated kidney cells within the glomerulus. Biomimetic fractal patterns derived from glomerular histology were used to generate topographical (2.5-D) substrates for cell culture. Podocytes grown on fractal topography expressed higher levels of functional markers and exhibited enhanced cell polarity. To track morphological complexities of differentiated podocytes, we employed a fluorescent labelling assay where labelled individual cells are tracked within otherwise optically silent confluent cell monolayer to reveal single-cell borders. RNAseq analysis suggested enhanced ECM deposition and remodeling in podocytes grown on fractal substrates versus flat surfaces, and enhanced maturation accompanied by stress in podocytes grown on fractal versus non-fractal topography. The incorporation of fractal topography into standard tissue culture well plates as demonstrated here may serve as a user-friendly bioengineered platform for high-fidelity cell culture.
Published in
Biomimetic fractal topography enhances podocyte maturation in vitro
Liu C, Aggarwal P, Wagner KT et al. · Nature communications 2025 · PMID 41398144 · doi:10.1038/s41467-025-66037-8
This dataset
Open GSE298416 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 GSE298416_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 PRJNA1269308 and SRA study SRP588483. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41398144) ↗
Study design
6 × E11 murine podocytes, RT, vs 6 × E11 murine podocytes, HF, vs 5 × E11 murine podocytes, NT,

Supports a between-group comparison across 17 samples.

How we read this: 3 replicated groups read from 17 sample titles; they account for 17 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
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