Single-cell RNAseq analysis (10X Genomics Chromium) of refilled lung interstium macrophages on day 4 after depletion

Lung interstitium macrophages (IMs) are non-alveolar resident tissue macrophages which contribute to the lung homeostasis. These cells were reported to be heterogeneous by our group and other teams, which contains two main distinct subpopulations: CD206+ IMs and CD206- IMs. However, the exact origin of IMs and the transcriptional programs that regulate IM differentiation remains unclear. In recent report, we analyzed the refilled IMs in the course of time after induced IM depletion with single-cell RNA sequencing (10X Genomics Chromium) and bulk RNA sequencing. The IMs in Day 4 post-depletion were compared to the those without depletion. Results showed that refilled IMs had a lower ratio of CD206+ IM vs CD206- subpopulation comparing to IMs without depletion, but they shared high similarity to each other, indicating that the de novo IM population had been established before Day 4 post-depletion. The lung IMs and monocytes were sorted from two groups of mice. Group “DT96h” contains 5 IM-DTR mice, which were treated with 50 ng diphtheria toxin (DT) 4 days before sacrifice. Group “NoTreatment” contains 5 litternate control mice without DT treatment. On the day of sacrifice, mice were sacrificed and lung monocytes and IMs were sorted by FACS and pooled before sending to 10X Chromium library construction. Processed data then were analyzed with Bioconductor and Seurat package.