Extended Data Fig. 3: RNA-seq reveals differences in chemokine activity and integrin mediated signaling between Grem1+ and Grem1− FRCs.
From: Gremlin 1+ fibroblastic niche maintains dendritic cell homeostasis in lymphoid tissues
a, Top: UMAP as in Fig. 1a), here colored by Cd200 expression. Bottom: Violin plot showing the expression of Cd200 in Grem1+ clusters 1 and 3 from Fig. 1a. b, Representative plots showing CD200 expression on EYFP+ (Grem1+) FRCs (FRC: CD45−Ter119−CD31−Madcam1−CD21/35− PDPN+) in skin draining lymph nodes (SLN) of Grem1-Cre-ERT2 Rosa26 EYFP mice (n = 4) post-tamoxifen induction c, Left: Representative plots showing CD90 and CD26 expression on EYFP− (Grem1−) CD34+ FRCs in SLN of Grem1-Cre-ERT2 Rosa26 EYFP mice (n = 4) at day 25 post-tamoxifen induction. Right: UMAP as in Fig. 1a, here colored by Cd34, Dpp4, and Thy1 expression. d, Relative average expression of 25 of the most up – and downregulated genes in bulk RNA-seq samples of Grem1+ and Grem1− FRCs. e, Heatmap of expression of marker genes (columns) determined via scRNA-seq [MAST, adj. p-val <0.05 in both replicates comparing Grem1+ FRCs to all other fibroblastic cells] in bulk RNA-seq samples of Grem1+ and Grem1− fibroblasts (rows). f, Gene set enrichment analysis comparing the distribution of the log2FC of Grem1+ vs Grem1− cells across all genes (blue) to the distribution of genes in indicated categories (orange); fry with p-value adjustment. g, Heatmap of genes (rows) from indicated gene ontology (GO) categories with significant (voom/limma, adj. p-val <0.05) differences in gene expression between Grem1+ and Grem1− bulk RNA-seq libraries (columns). h, Enrichment of transcription factor binding sites in genes with significant (MAST, adj. p-val <0.05) upregulation in Grem1+ FRCs compared to Grem1− FRCs in scRNA-seq. i, Volcano plot visualizing the fold-change (x-axis, log2 transformed) and adjusted p-value (y-axis, Spectronaut adjusted p-val <0.001) for proteins (dots) between Grem1+ and Grem1− cells. j, Comparison of indicated proteins from proteomic analysis between Grem1+ and Grem1− FRCs. Data are representative of two independent experiments (b, c); data are compilation of proteomic analysis from three independent sorts (j). ***P < 0.001, **P < 0.01, *P < 0.05 (two-tailed unpaired Student’s t-test). Exact P-values in extended source data. Data are shown as mean ± SEM.
