We report cell type specific Nova HITS-CLIP using BAC-transgenic lines expressing GFP-Nova under the motor neuron specific choline acetyltransferase (Chat) promoter. By comparing transcriptome wide Nova binding map in motor neurons and that in the whole spinal cord, we identified differential Nova binding sites in motor neurons, which correlate with motor neuron specific RNA processing. Overall design: 14 total samples were analyzed. For HITS-CLIP, 4 biological replicates were performed for each BAC-transgenic line, as well as the whole spinal cord. For RNA-seq, 2 biological repliates were performed on the whole spinal cord.