GEO series

Comparative analysis of chromatin accessibility during chondrogenesis and in osteoarthritis

GSE270602 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 26 samples Submitted 2025/01/01 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 26 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 26 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.
Paper: Chromatin accessibility in MSC chondrogenesis, adult hip cartilage chondrocytes and osteoarthritisOsteoarthritis and cartilage · 2026

Summary (written by the submitters)

To reveal the organisation of the cartilage cell chondrocyte genome and identify changes that occur within this organisation during development and due to osteoarthritis (OA). Methods Assay for Transposase -Accessible Chromatin using Sequencing (ATAC-seq) was performed on chondrocytes isolated from 16 patients undergoing total hip replacement because of OA (n=7) or due to a neck of femur fracture (NOF, n=9).

Read the full summary ↓

ATAC-seq was similarly performed on bone-marrow mesenchymal stem cells (BM-MSC) and differentiated chondrocytes of two donors. DNA sequence reads (av. 50 million/sample) were aligned to human genome Hg38. Peaks were called using MACS2 and differential accessibility identified by DiffBind. Interexperiment comparisons and intersection with published gene expression changes, chondrogenesis ChIP-seq, knee ATAC-seq and human tissue scATAC-seq were performed in Galaxy and R. OA GWAS signal regions were overlapped with our defined chondrocyte ATAC-seq peaks. Results In BM-MSC and derived chondrocytes we mapped 138005 open chromatin regions, of which 20979 and 50699 significantly increased and decreased respectively during cell differentiation. In hip chondrocytes we identified 115295 open chromatin regions, 1383 and 573 were more or less differentially accessible respectively when comparing OA with NOF samples. In both data sets ‘newly accessible regions were enriched at enhancer regions (defined by ChIP-seq). Comparing the data with the ATAC-seq from the single cell ATLAS we identified 11866 open regions exclusive to chondrocytes. Genes associated with these regions were significantly enriched for cartilage-related gene ontology terms. Taking the 420 OA GWAS signals present in the GWAS catalogue, 313 of the OA regions (defined as lead SNP + proxy SNPs with r2 ≥ 0.8) overlapped with a chondrocyte ATAC-seq region. Conclusions Here we have mapped chromatin accessible region changes during chondrogenesis, showing that newly accessible regions are enriched at enhancer regions and positively correlate with gene expression. Open chromatin region changes between OA and NOF cartilage were fewer, and peak differences were subtle. Overall, we have associated OA GWAS loci with accessible regions and defined regions of the genome specific to cartilage and chondrogenesis.

Published in

Chromatin accessibility in MSC chondrogenesis, adult hip cartilage chondrocytes and osteoarthritis

Barter MJ, Soul J, Cheung K et al. · Osteoarthritis and cartilage 2026 · PMID 41512915 · doi:10.1016/j.joca.2025.12.015

This dataset

Open GSE270602 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE270602_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1127542 and SRA study SRP515828. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41512915) ↗

Study design

6 conditions, mostly in triplicate

NOF, Patient ×9 OA, Patient ×7 MSC 2454E, Day0, ×3 MSC 2454E, Day14, ×3 MSC 8A, Day0, ×2 MSC 8A, Day14, ×2

Supports a between-group comparison across 26 samples.

How we read this: 6 replicated groups read from 26 sample titles; they account for 26 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

GSM8348164 MSC 2454E, Day0, Replicate1 MSC 2454E, Day0,
GSM8348165 MSC 2454E, Day0, Replicate2 MSC 2454E, Day0,
GSM8348166 MSC 2454E, Day0, Replicate3 MSC 2454E, Day0,
GSM8348167 MSC 2454E, Day14, Replicate1 MSC 2454E, Day14,
GSM8348168 MSC 2454E, Day14, Replicate2 MSC 2454E, Day14,
GSM8348169 MSC 2454E, Day14, Replicate3 MSC 2454E, Day14,
GSM8348170 MSC 8A, Day0, Replicate1 MSC 8A, Day0,
GSM8348171 MSC 8A, Day0, Replicate2 MSC 8A, Day0,
GSM8348172 MSC 8A, Day14, Replicate1 MSC 8A, Day14,
GSM8348173 MSC 8A, Day14, Replicate2 MSC 8A, Day14,
GSM8348174 NOF, Patient1 NOF, Patient
GSM8348175 NOF, Patient2 NOF, Patient
GSM8348176 NOF, Patient3 NOF, Patient
GSM8348177 NOF, Patient4 NOF, Patient
GSM8348178 NOF, Patient5 NOF, Patient
GSM8348179 NOF, Patient6 NOF, Patient
GSM8348180 NOF, Patient7 NOF, Patient
GSM8348181 NOF, Patient8 NOF, Patient
GSM8348182 NOF, Patient9 NOF, Patient
GSM8348183 OA, Patient1 OA, Patient
GSM8348184 OA, Patient2 OA, Patient
GSM8348185 OA, Patient3 OA, Patient
GSM8348186 OA, Patient4 OA, Patient
GSM8348187 OA, Patient5 OA, Patient
GSM8348188 OA, Patient6 OA, Patient
GSM8348189 OA, Patient7 OA, Patient

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