(A, top) Metabolic genes with differential expression between proximal and distal BP regions. Data show normalised RPKM values in the proximal and distal BP regions at E6. (A, bottom) Affymetrix microarray data showing the fold change in expression of each transcript at the proximal compared to the distal region of the BP at E14. (B) Sectioning protocol used to collect samples from proximal and distal regions at E8. Proximal and distal tissue used for RNA scope was collected and processed simultaneously from within the same BP. (C, D) RNA scope analysis of genes encoding metabolic regulatory proteins in the developing BP identified in A. Images show gene expression in comparative cross-sections from proximal and distal BP regions at E8. Bmp7 expression was used as a control for tonotopic identity as we know it is expressed in a distal-to-proximal gradient. (E–H) Quantification of RNA scope fluorescence in the BP at proximal and distal regions. The sensory domain (sd) and tegmentum vasculosum (v) were identified morphologically using the DAPI (4′,6-diamidino-2-phenylindole) channel. Bmp7 – Bone morphogenetic protein 7, Got2 – Glutamic-Oxaloacetic Transaminase 2, Sdhd – Succinate dehydrogenase complex subunit D, Aco2 – Aconitase 2, Ldhb – Lactate dehydrogenase beta, Pkm2 – Pyruvate kinase M2, Ldha – Lactate dehydrogenase alpha, Nnt – Nicotinamide Nucleotide Transhydrogenase, Idh3b – Isocitrate dehydrogenase beta, Idh3a – Isocitrate dehydrogenase alpha. Transcripts annotated red indicates those involved in regulating cellular NADPH/NADH. Data are mean ± standard error of the mean (SEM), * p< 0.05, **p < 0.001 two-way analysis of variance (ANOVA).