Fig. 1

Multiomic transcriptional and epigenetic single-cell analysis of SFs. A Schematic representation of the experimental workflow. We collected ankle synovial tissue from wt and hTNFtg mice, enzymatically disaggregated the tissue, and sorted the cells into one gate representing fibroblasts (CD45−, Ter119−, CD31−, Pdpn+). We profiled the cells with both sc 3′ RNA-seq and ATAC-seq using 10X technology and performed scRNA-seq, scATAC-seq, and cross-species integrative analyses with publicly available human RA datasets. B High-quality filtered synovial fibroblasts (n = 5903 for the scRNA-seq and n = 6046 for the sc-ATAC-seq) projected in UMAP space and colored by cluster assignment. C Feature plots on the UMAP embeddings of the SFs shown in B, displaying normalized expression values (for scRNA-seq) and gene activity scores (for scATAC-seq) for Prg4 and Thy1 genes. D Similar to B, but cells are colored by the sample of origin. E scRNA-seq heatmap showing the average scaled expression values for the upregulated genes of each subpopulation (upper panel) and scATAC-seq heatmap of differentially upregulated accessible peaks (lower panel). F Pearson correlation of scaled expression values (RNA) and activity scores (ATAC), followed by hierarchical clustering, for the most variable genes identified in the scRNA-seq analysis