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scMultiome-seq and single-cell spatial HD data for the developing human knee

GSE260926 Homo sapiens Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other 5 samples Submitted 2025/11/26 Platform GPL20301Platform GPL34281Platform GPL24676
Summary
Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. Compromises to the integrity of joint-lining articular cartilage in particular lead to debilitating chronic degenerative diseases including osteoarthritis. To better understand how human articular cartilage develops in vivo, we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femora at 2 fetal timepoints. We used these multiomic data to predict transcription factor-based regulatory networks that are important for articular chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and identified new biological roles for CREB5. We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro.
Published in
Leveraging single cell multiomic analyses to identify gene regulatory networks that drive human articular cartilage cell fate
Jachim SK, Venkatasubramanian D, Senevirathne G et al. · Osteoarthritis and cartilage 2026 · PMID 41520766 · doi:10.1016/j.joca.2025.12.025
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Direct links to NCBI, no account and no request form: the whole study as GSE260926_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 5 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1084014 and SRA study SRP493468. Searching any of these in the dataset finder brings you back here.

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