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The aim of this study was to analyze the transcriptome of TER119–CD31–CD45–CD51+CD200+CD105– population (further, CD200+), potential early osteocondroprogenitors, whose frequency is reduced in the joints of mice with antigen-induced arthritis (AIA) [1]. A population defined by similar surface markers has been previously identified as murine skeletal stem cells in bone [2]. In order to confirm their identity this population was compared to TER119–CD31–CD45–CD51+CD200–CD105+ (further, CD105+) cells, which possibly represent committed progenitors, or other non-progenitor population such as synovial fibroblasts. In order to asses changes in CD200+ population in inflammatory setting, it was also compared to the same population from healthy mice. AIA was induced by immunization of mice with methylated bovine serum albumin (mBSA) and subsequent intra-articular injection of mBSA, while non-immunized mice were injected with phosphate-buffered saline at all timepoints. Ten days after intra-articular injection, knee joints were harvested and synovial cells were released by collagenase digestion. Using fluorescence-activated cell sorting, 200–500 cells from selected populations were sorted directly into cell lysis buffer, RNA was reversely transcribed, and first strand cDNA product was amplified. cDNA amplicons were used for library preparation. Bioinformatics analysis was performed using cutadapt [3], HISAT2 [4], Samtools [5] and StringTie [6] tools, and egdeR [7], limma [8], and ClusterProfiler [9] Bioconductor packages. In addition to access to raw data at the NCBI Gene Expression Omnibus repository, this article also provides sample similarity analysis, tables of differentially expressed genes, graphic visualisations of differential expression and gene set enrichment analysis performed on publicly available GO terms. Interpretation of osteochondroprogenitor phenotype of CD200+ population based on analysis of presented data is provided in the article “What do we know about bone morphogenetic proteins and osteochondroprogenitors in inflammatory conditions?” [10]. Reuse of this data may help researchers elucidate alterations of synovial stromal and osteochondroprogenitor populations in inflammatory settings and define their role in structural damage in rheumatoid arthritis.