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. Overall design: 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.