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3D fractal topography attenuates inflammation and confers resilience to glomerular podocytes

GSE300321 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/12/21 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 18 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
Homo sapiens (human)
Samples
18 samples: 6 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.
Summary (written by the submitters)
In vivo, podocytes wrap around a looping capillary forming interdigitations required to establish a barrier function in kidney filtration. Cultured human podocytes can mimic key in vivo disease-associated changes—such as junctional and cytoskeletal remodeling, but their intricate, self-similar 3D branching structure remains poorly understood and technically difficult to replicate in vitro, especially in the context of inflammatory injury.
Read the full summary ↓
Here, we established 3D fractal hemispheres capturing key features of glomerular architecture using nanoscale two-photon polymerization (2PP), enabling a detailed investigation into the effects of 3D topographies with various fractal indices on podocyte morphology and function. Podocytes cultured on intermediate fractal hemispheres, exhibited enhanced cytoskeletal branching, increased expression of slit diaphragm markers, and upregulation of nephrogenesis-related genes. To explore cellular responses to inflammatory stimuli by TNF-α and IL-6, we established a culture of fluorescently labelled podocytes within otherwise optically silent monolayer. The changes of single podocyte structure, fractal dimension and RNA sequencing revealed that podocytes grown on intermediate fractal hemispheres exhibited an enhanced immunosuppressive response, highlighting the potential of fractal topological structures in mitigating inflammation induced podocyte damage and kidney disease progression. A co-culture system with reporter THP-1-derived macrophages demonstrated a pronounced shift toward the M1 macrophage phenotype and heightened activation of inflammation pathways when podocytes were co-cultured on smooth hemispheres, compared to those on intermediate fractal hemispheres. These findings suggest that fractal microenvironments may play a crucial role in modulating podocyte-macrophage interactions and inflammatory responses in kidney disease.
This dataset
Open GSE300321 in finder → Find more human 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 GSE300321_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 PRJNA1280089 and SRA study SRP593502. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
PODO/TERT256 human podocytes, smooth topograp… ×3 PODO/TERT256 human podocytes, fractal topogra… ×3 PODO/TERT256 human podocytes, smooth topograp… ×3 PODO/TERT256 human podocytes, fractal topogra… ×3 PODO/TERT256 human podocytes, smooth topograp… ×3 PODO/TERT256 human podocytes, fractal topogra… ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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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