HuD CLIP in spinal cord
CLIP libraries were prepared using an HuD antibody following the standard HITS-CLIP prototcol (Moore et al. Nat Protocols, 2014, 9:263-293).  3' linker ligation was performed using adaptor MSFP3 (5'-CAAGCAGAAGACGGCATACGAGATCCGCTGGAAGTGACTGACAC-3').  5' linker ligation was performed using Anchor_MiSeq_CTAG_RL5_1  (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCTAGAGGGAGGACGATGCGG-3') for the Sod1_WT_spinalcord sample, and Anchor_MiSeq_GATC_RL5_2  (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGATCAGGGAGGACGATGCGG-3') for the Sod1_MUT_spinalcord sample.  The libraires were sequenced on Illumina MiSeq to obtain 151 nt reads.  The raw sequencing data was de-multiplexed and processed using the CTK pipeline (Shah et al. Bioinformatics, 2017).