HuBMAP: High Resolution 3D Mapping of Cellular Heterogeneity Within Multiple Types of Mineralized Tissues

The overall goal of the study was to generate 3D single cell maps of healthy human knee cartilage. Articular cartilage from the weightbearing and non-weightbearing regions of the femoral condyles in healthy knees from young donors (n=12) was analyzed by bulk RNA-sequencing (RNA-Seq), single nuclei RNA (snRNA-seq) and ATAC-sequencing and by spatial transcriptomic methods (GeoMx, MERFISH and Xenium). These multimodal data and additional single cell RNA-sequencing (scRNA-seq) data were integrated to generate a comprehensive molecular, genomic and function annotation of chondrocyte populations. Regulatory mechanisms were derived by linking motifs in expressed genes, transcription factors and chromatin organization.]]>
Inclusion Criteria Donors both male and female up to 55yo with normal macroscopic scores of the knee cartilage Post-mortem interval: 48 hours History of IV drug use and cancer are not excluded.Exclusion Criteria HIV, Syphilis, and Hepatitis A, -B, -CSepsis Knee replacement or other knee surgery Any knee arthritis diagnosis Immobility (complete bed rest) for more than 2 weeks ]]>
Donor recruitment (n=12) and tissue collection (osteochondral tissue from weightbearing and non-weightbearing medial femoral condyle) have been completed at Scripps Research. We are performing bulk RNA-sequencing (cartilage and subchondral bone separately) for 12 donors, 10x multiome single nuclei for 12 donors (cartilage only), GeoMx spatial transcriptomics for 12 donors (osteochondral) and mRNA FISH for 8 donors (cartilage only). From a prior study, 7 donors were used for 10x Single Cell RNA-sequencing data on cartilage and meniscus tissues.]]>