Extended Data Fig. 4: 10X Chromium single-cell RNA sequencing (droplet-based single-cell) analysis of CD45− cell populations from inflamed synovium.
From: Distinct fibroblast subsets drive inflammation and damage in arthritis
a, t-SNE projection of non-haematopoietic stromal cells from the inflamed mouse joint (n = 3 biological replicates, day 9 STIA) showing the initial automatic cluster assignments from Seurat (projection is identical to that shown in Fig. 3a). b, The same t-SNE plot coloured by biological replicate. c, The bar plot shows the number of cells in each cluster stratified by replicate. d, Cluster cell identification: the five panels of violin plots show expression (normalized, log-transformed counts of the cells from all of the n = 3 biological replicates, y axes) of known cell-type marker genes (for fibroblasts, LL fibroblasts, osteoblasts, chondrocytes and vascular cells) in each of the automatically assigned clusters (x axes). The colours of violin plots correspond to those shown in Extended Data Fig. 4a.
