Fig. 4: Detailed characterization of the macaque spiral ganglion neurons.
From: Molecular heterogeneity of the non-human primate cochlea
a Left: Highlighted SGN subclass from the whole macaque cellular map in the UMAP plot. Right: UMAP plot depicting 4 subtypes after joint-embedding and re-clustering of the macaque SGN subclasses (type I and II), which was re-clustered using scANVI (single-cell ANnotation using Variational Inference)-based integration. b A dot plot illustrating the variance-scaled, log-transformed expression of SGN subtype markers (x-axis) identified in mouse species for comparison between macaque and mouse SGN subtype cells (y-axis). C Immunofluorescence images demonstrating CALB2 (calretinin) associated with CALB1 (calbindin) localization in 5-year-old macaque (top) and 3-week-old mouse (bottom) SGNs. n = 3 independent experiments with similar results. d Same as in (c), but for CALB1 associated with GATA3 (trans-acting T-cell-specific transcription factor GATA-3) or PRPH (peripherin) localization in 5-year-old macaque SGNs. Arrowhead highlighted the co-localization of CALB1 with GATA3 or with PRPH in macaque SGNs, respectively. n = 3 independent experiments with similar results. e, g Dot plots showing the variance-scaled, log-transformed expression of transcription factors (TFs, x-axis) with mutually exclusive expression in type I (e) or in type II SGNs (g) in macaque and mouse snRNA-seq data (y-axis). f Representative images of RNAscopeTM plus immunofluorescence demonstrating TUBB3 associated with PROX1 (prospero homeobox protein 1) or with RUNX1 (Runt-related transcription factor 1) localization in 5-year-old macaque SGNs. n = 3 independent experiments with similar results. h Representative images of immunofluorescence demonstrating TUBB3 associated with SMAD1 (mothers against decapentaplegic homolog 1) localization in 5-year-old macaque SGNs and 3-week-old mouse SGNs, respectively. n = 3 independent experiments with similar results. i A dot plot illustrating the PBX3 (pre-B-cell leukemia transcription factor 3) expression level in SGN subtypes, stratified by species. The expression level was calculated with variance-scaled, log-transformed normalization. j Bar plot presenting selected results from the Gene Ontology (GO) analysis of type II macaque-enriched DEGs involved with PBX3 in different biological processes. k Representative images of immunofluorescence showing PBX3 localization in 5-year-old macaque SGNs (left) but not in 3-week-old mouse SGNs (right). n = 3 independent experiments with similar results.
