Position Specific Alternative Splicing and Gene Expression Profiles along the Tonotopic Axis of Chick Cochlea

We performed an RNA-Seq experiment for three sample groups on base, middle, and apex regions of chick cochlea to identify genes and splicing events whose regulation mechanisms are associated with tonotopy. We conducted transcriptome-wide gene expression profiling and AS analysis using high-throughput sequencing. Post-hatch day 1 chickens were euthanized by carbon dioxide inhalation followed by decapitation. The head was hemi-sectioned and the cochlea duct was isolated in cold DEPC-treated PBS. The basilar papilla was dissected from the cochlear duct and divided into three pieces: base, middle, and apex. Each piece was collected separately and quickly frozen to minimize RNA degradation. Total RNA from 12 chickens (24 cochleas) were used for 3 biological replicates for each region.