Transcriptomic response in osteoarthritis determined by single-cell RNA sequencing in a naturally occurring equine model

We used single-cell RNA sequencing to characterize the heterogeneity of equine synovial fluid and synovial tissue in a healthy and osteoarthritic joints. The complete dataset consists of 150bp paired end sequencing data obtained using a 10x Genomics single-cell RNA sequencing platform (Chromium Next GEM Single Cell 3ʹ Kit v3.1 protocol). The final dataset consists of data from 4 biologically distinct horses. Synovial fluid samples were collected from an osteoarthritis (OA) affected joint and the contralateral normal joint for the following library pairs: sf_normal_1+sf_oa_1 and sf_normal_2+sf_oa_2. The remaining two synovial fluid samples were obtained from biologically distinct horses, one from an OA affected joint (sf_oa_3) and one from an unaffected normal joint (sf_normal_3). The final two libraries (syn_normal_1+syn_oa_1) were synovial tissue samples obtained from the same horse from which the sf_normal_2+sf_oa_2 libraries were prepared; syn_normal_1 was collected from the unaffected normal joint while syn_oa_1 was collected from the OA affected joint.