Fig. 1: A single-cell transcriptomic atlas of the macaque cochlea.

a, b Workflow for the droplet-based 10× single-nucleus RNA (snRNA) sequencing platform on juvenile (1-year-old) and adult (5/11-year-old) macaque cochleae. The cellular components in the whole cochlea organ illustrated in (a), adopted and modified by Jean et al. PNAS 2023, which include basal stria cells (Bs), root cells (Rt), intermediate stria cells (Is), spindle cells (Sp), marginal stria cells (Ms), endothelial cells (Endo.cells), pericytes, smooth muscle cells (SMC), pillar cells (PC), Deiters’s cells (DC), inner border cells (IBC), inner phalangeal cells (IPh), Hensen’s cells (HeC), interdental cells (IDC), Claudius cells (CC), inner sulcus cells (ISC), outer sulcus cells (OSC), inner hair cells (IHC), outer hair cells (OHC), type I spiral ganglion neurons (TypeI SGN), type II spiral ganglion neurons (TypeII SGN), satellite glial cells, Schwann cells, osteocytes (OB), Reissner’s membrane (RM), tympanic border cells (TBC), and fibrocytes (Fb). c A timeline for displaying macaque cochlea sampling across ages for snRNA-seq, cell-type validation, and electrophysiological recording. A total of 4 macaque cochleae were used for sequencing and of 4 macaque cochleae were used for validation and one for patch-clamping. d Uniform Manifold Approximation and Projection (UMAP) representation of whole-organ cochlear profiles identified more than 20 distinct cochlear cell types. A total of 36, 701 nuclei captured were from 4634 nuclei for the 1-year-old macaque, 27,616 nuclei for the 5-year-old macaques and 4451 nuclei for the 11-year-old macaque, respectively. We used scVI (single-cell variational inference) for this batch-corrected integration. e Dot plot displaying the variance-scaled, log-transformed expression of well-characterized marker genes (y-axis) used for manual annotating each cell type (x-axis). Among this, Pan_SC refers to marker genes that are enriched in supporting cells in cochlear epithelium. f Immunofluorescence results confirming the expression of hair cell markers, including CALB1 (Calbindin) and OTOF (Otoferlin), and the auditory neuronal marker CALB2 (Calretinin) in the 5-year-old macaque cochlea and the P21 mouse cochlea, respectively. n = 3 independent experiments with similar results.