Fig 1: Isolation of cell type-specific transcripts from both HCs and tissue macrophages in the Gfi1-Cre RiboTag model. (A) Identification of macrophage-specific transcripts was achieved by comparing differentially expressed genes (DEGs) from whole utricle Gfi1-Cre RiboTag IPs (top) to those from utricles in which the stroma (containing resident macrophages) had been removed from the sensory epithelium, yielding a stroma-free isolated sensory epithelium (bottom). Shown are transcripts from HCs (red), SCs (blue), stroma (beige), and macrophages (purple). (B) Comparison of whole utricle Gfi1-Cre IP to input DEGs revealed enrichment for both hair cell and macrophage markers. Scatterplot shows Log2FC values vs. normalized transcript abundance from DEG comparison of the whole tissue Gfi1-Cre IP to the input. Markers of HC type (Myo3a, Atoh1, Calb1, Ocm, Pvalb, Gfi1, Calb2, Bdnf, Otof) are shown in red and labeled along with markers of tissue macrophage cell type shown in purple [Itgam (CD11b), Ptprc (CD45), Cx3cr1, Adgre1 (F4/80)]. (C) Comparison of whole tissue (sensory epithelium plus stroma, purple) to isolated sensory epithelium (without stroma, red)DEGs revealed macrophage markers. Scatterplot shows Log2FC values vs. normalized transcript abundance from DEG comparison of the whole tissue Gfi1-Cre IP to the isolated sensory epithelium Gfi1-Cre. Markers of HC type (Otof, Cdh23) are labeled along with markers of tissue macrophage cell type [Itgam (CD11b), Ptprc (CD45), Cx3cr1, Adgre1 (F4/80)].