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OSR1 and SIX2 Drive Divergent Transcriptional Programs in Human Kidney Cells: Implications for Regeneration and Tumorigenesis\

GSE309076 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2025/09/26 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 13 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
13 samples: 5 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
OSR1 and SIX2 drive divergent transcriptional programs in human kidney cells: implications for regeneration and tumorigenesisFrontiers in bioengineering and biotechnology · 2025
Summary (written by the submitters)
During human nephrogenesis, nephron progenitor cells generate approximately one million nephrons. We investigated the effects of ectopic expression of OSR1 and SIX2, both individually and in combination, in adult human kidney cells. OSR1 and SIX2 induced distinct reprogramming programs with differential functional outcomes. SIX2 overexpression maintained epithelial morphology while significantly enhancing proliferation and clonogenic efficiency.
Read the full summary ↓
Transcriptionally, SIX2 established epithelialization and cell cycle networks, downregulating proximal tubule markers, while upregulating distal nephron markers and proliferation genes. In vivo, SIX2-expressing cells formed organized tubular structures with distinct luminal architecture. In contrast, OSR1 overexpression induced morphological changes and activated developmental morphogenetic pathways but did not enhance proliferation and showed minimal tubulogenic capacity. RNA sequencing analysis revealed coordinated changes in nephron segment-specific markers and activation of distinct transcriptional programs.\
Published in
OSR1 and SIX2 drive divergent transcriptional programs in human kidney cells: implications for regeneration and tumorigenesis
Pode-Shakked N, Cohen-Zontag O, Omer D et al. · Frontiers in bioengineering and biotechnology 2025 · PMID 41112069 · doi:10.3389/fbioe.2025.1645499
This dataset
Open GSE309076 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 GSE309076_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 PRJNA1333921. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41112069) ↗
Study design
5 conditions, mostly in triplicate
Human kidney epithelial cells mCherry control ×3 Human kidney epithelial cells SIX2 overexpres… ×3 Human kidney epithelial cells OSR1 overexpres… ×3 Human kidney epithelial cells naive ×2 Human kidney epithelial cells OSR1+SIX2 doubl… ×2

Supports a case/control comparison: 8 samples read as cases, 5 as controls.

How we read this: 5 replicated groups read from 13 sample titles; they account for 13 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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