Atoh1b-dependent genes in early zebrafish inner ear development

Identification of genes regulated by the distal-less homeodomain transcription factor Atoh1b. To this aim, we performed gene expression profiling analysis using data obtained from RNA-seq of 3 samples each from wt control as well as atoh1b knockdown. Generation of a transcriptome dataset of control and Atoh1b-depleted zebrafish embryos using the pax8:DsRed transgene, which labels the developing OEPD and kidney anlagen. At OEPD stages, we performed fluorescence-activated cell sorting (FACS) and the isolated transcripts from sorted cells of control and Atoh1b-depleted embryos were used for transcriptome profiling. Comparison of control versus Atoh1b-depleted samples reveals numerous differentially expressed genes.