Integrated transcriptomic and epigenomic profiling of mouse lung cells at the single-cell level

Our previous scRNA-seq data suggest that immune and stromal cells exhibit memory properties that contribute to the long-term regulation of lung allergic responses, which are cross-regulated by the co-administration of TLR ligands or bacterial extracts. To further investigate these mechanisms, we performed single-cell multiome sequencing (scMulti-omics) to integrate transcriptomic and epigenomic profiling, focusing on the characterization of immune and stromal cell populations during long-term resolution. Overall design: To assess long-term changes induced by allergen exposure and cross-regulation, we performed scMulti-omics on whole lung cells from mice under four conditions: Long-Term Phase (6 Weeks): Control, papain, papain+CpG or papain+OM85, analyzed 6 weeks post-administration (no recall).