Dlx3b/4b-dependent genes in early zebrafish inner ear development

Identification of genes regulated by the distal-less homeodomain transcription factors Dlx3b and Dlx4b (Dlx3b/4b). 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 dlx3b/4b knockdown. Generation of a transcriptome dataset of control and Dlx3b/4b-depleted zebrafish embryos using the pax8:DsRed transgene, which labels the developing OEPD (otic-epibranchial progenitor domain) and kidney anlagen. At OEPD stages, we performed fluorescence-activated cell sorting (FACS) and the isolated transcripts from sorted cells of control and Dlx3b/4b-depleted embryos were used for transcriptome profiling. Comparison of control versus Dlx3b/4b-depleted samples reveals numerous differentially expressed genes.