Single-cell RNA-seq of endothelial and pericyte populations in the mouse cochlear stria vascularis

The cochlear stria vascularis (SV) maintains the endocochlear potential and relies on specialized vascular endothelial cells and pericytes. To characterize the transcriptional profiles of these vascular populations at single-cell resolution, we performed single-cell RNA sequencing (scRNA-seq) on SV tissue from reporter mice. SV was microdissected from temporal bones of 1–3 month-old Tie2-GFP (endothelial reporter) and NG2-DsRed (pericyte reporter) mice, enzymatically dissociated to obtain single-cell suspensions, and, when applicable, subjected to FACS enrichment for Tie2-GFP–positive endothelial cells or NG2-DsRed–positive pericytes. Viable cells were loaded onto the 10x Genomics Chromium platform for single-cell capture and 3' barcoded library preparation. This dataset contains two independent batches corresponding to SV endothelial cell–enriched and pericyte-enriched preparations and enables analysis of vascular heterogeneity within the mouse stria vascularis. Overall design: Two independent single-cell RNA-seq batches from the 1-3 months mouse cochlear stria vascularis were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq. Batch 1. Endothelial cell–enriched batch (Tie2-GFP) Batch 2. Pericyte-enriched batch (NG2-DsRed)