Science Immunology

Supplementary Materials

The PDF file includes:

  • Fig. S1. Quality control of scRNAseq data.
  • Fig. S2. Differential expression and quality control metrics show clusters grouped on nondesirable traits.
  • Fig. S3. Precursor clusters show similarities across condition.
  • Fig. S4. scRNAseq reveals that canonical M1 and M2 markers do not correlate with single-cell clusters.
  • Fig. S5. Macrophage gating scheme for regenerative subsets.
  • Fig. S6. Macrophage gating scheme for fibrotic subsets.
  • Fig. S7. Murine macrophage CD9 and CD301b profiles using flow cytometry.
  • Fig. S8. Differential gene expression heatmap for RP3 and R2.
  • Fig. S9. Cell composition of clusters by experimental condition.
  • Fig. S10. Expression of inflammatory genes in fibrotic cluster F2.
  • Fig. S11. Quantification of expression levels of CD11c and CD206.
  • Fig. S12. RNA velocity analysis.
  • Fig. S13. Regenerative subsets R1 and R2 phagocytosis assay.
  • Fig. S14. Immunofluorescence microscopy of F4/80+CD301b+ macrophages.
  • Fig. S15. Cluster R3 expresses tissue-specific genes.
  • Fig. S16. Expression of inflammatory genes in fibrotic cluster F2.
  • Fig. S17. Immunofluorescence microscopy on F4/80+CD9+ macrophages.
  • Fig. S18. In vitro TH17 dependence of Il36γ expression in macrophages and IL-36γ induction of fibrosis phenotypes in cultured fibroblasts.
  • Fig. S19. Analysis pipeline for publicly available datasets.
  • Fig. S20. Scheme to generate for tSNE projection for virtual aggregate flow cytometry data.
  • Fig. S21. Scaling metric for the scRNAseq raw data.
  • Fig. S22. Variance by principle component.
  • Fig. S23. Expression of fibroblast signature genes in small contaminant cluster.
  • Table S1. Quality control metrics for 10× scRNAseq.
  • Table S2. Macrophage FACS panel.
  • Table S3. Macrophage subtype panel.
  • Table S4. Murine TaqMan gene expression assay probes.
  • Table S5. Human TaqMan gene expression assay probes.
  • Table S6. Sorted cell populations for NanoString Gene Expression Profiling.
  • Legend for table S7

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Other Supplementary Material for this manuscript includes the following:

  • Table S7 (.csv format). Differentially expressed genes for scRNAseq clusters.

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