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Uhrf1 determines osteophyte fate by regulating differentiation of synovial mesenchymal progenitor cells

GSE296850 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2026/05/12 Platform GPL22790
At a glance

RNA-seq (gene expression) · human · 10 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
10 samples: 5 × Human knee synovial cells siCtrl vs 5 × Human knee synovial cells siUHRF1Groups 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)
This study investigates the role of Uhrf1 in osteophyte formation, building on previous findings of the role of Uhrf1 in cartilage proliferation and chondrogenic differentiation. We used mesenchymal stem cell-specific Uhrf1 knockout (cKO) mice to evaluate osteophyte development and cartilage degeneration at 2 and 12 weeks post-DMM surgery.
Read the full summary ↓
At 2 weeks, cKO mice had significantly smaller osteophytes with reduced width, area, and maturity scores compared to controls. At 12 weeks, despite similar maturity scores, osteophytes in cKO mice were still smaller, and cartilage degeneration was more severe. Uhrf1 knockdown in human synovial cells led to decreased proliferation and chondrogenic differentiation. These results suggest that Uhrf1 is essential for early osteophyte formation and chondrogenesis, with its effects continuing as osteophytes mature. Additionally, osteophytes seem to protect against cartilage degeneration in OA, and RNA-seq analysis revealed that Uhrf1 deficiency upregulates genes that negatively affect cell devel
This dataset
Open GSE296850 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 GSE296850_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 PRJNA1261812 and SRA study SRP584535. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × Human knee synovial cells siCtrl vs 5 × Human knee synovial cells siUHRF1

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.