RNA-seq analysis of Barhl1 locus mutant mouse embryonic stem cell (mESC)-derived hair cell-like cells

Although Barhl1 has been known to be essential for the maintenance of cochlear hair cells, the precise molecular function of Barhl1 in hair cells has not been well studied. This study examined differentially expressed genes in Barhl1 locus mutant hair cell-like cells relative to wild type hair cell-like cells. We detected the critical expression time and period of Barhl1 in our in vitro hair cell induction system, and used the day 9 cultures during induction of otic progenitors towards hair cell-like cells to perform RNA-seq. The known hair cell-specific genes that were significantly downregulated in Barhl1 locus mutant hair cell-like cells are associated with hair cell functions and development, such as neurotransmitter secretion, calcium ion transport, intermediate filament bundle assembly, synaptic potential and sensory perception of sound. Overall design: mRNA profiles of induced hair cell-like cells derived from wild type (WT)-, Barhl1 mutant (BM)- and E3 E-box site mutant (BEM)-mESCs were generated by deep sequencing using Illumina HiSeq 4000.