Figure 1: HC transcriptome analysis.

(a) Representative images from an inner ear of an Atoh1/nGFP mouse. All HCs in the auditory and vestibular systems are GFP(+). Co-cochlea; Cr-crista; S-saccule; U-utricle. Scale bar, 50 μm. (b) Schematic diagram of cochlear and vestibular sensory epithelia, illustrating the cells designated as HC, ENHC and NECs in each organ. (c) Representative image of flow cytometry from cochlear epithelia of newborn Atoh1/nGFP mice. Left upper quadrant—pre-sorting figure: HCs are double positive (DP), ENHCs are positive for CD326 (SP), NECs are negative for CD326 and GFP (DN). Post-sort analyses of sorted cells showing a cell type-specific purity >94% for HCs, >99% for NECs and >98% for ENHCs. (d) Hierarchical clustering, based on all the expressed genes in the data set, separated the probed samples into three major branches according to cell type: HC, NEC and ENHC (c-cochlea and v-vestibular samples). (e) Two major clusters containing genes whose expression is elevated in HCs. Each cluster is represented by the mean pattern of its genes’ expression levels (error bars: ±s.d. calculated over all genes assigned to each cluster). Expression levels of each gene were standardized (mean=0, s.d.=1) prior to clustering. This methodology enabled grouping of genes that share similar patterns, but not necessarily the same magnitude of expression. The entire set of clusters is shown in Supplementary Fig. 2. (f) Enriched GO categories with a P value <0.01 (hypergeometric test) after false discovery rate correction for multiple testing. (g) Marker genes specific for cochlear HCs (top) and vestibular HCs (bottom) as detected in the expression microarray data set (left) and confirmed by the RNA-seq data set (right). Red represents enrichment, Green represents depletion. Data represent results from three biological replicates.