NONO knockdown RNA-seq and neuroblastoma PARCLIP analysis of NONO

siRNA knockdown of NONO mRNA followed by RNA-seq was carried out in the KELLY neuroblasotma cell line. In order to determine potential regulatory targets of NONO protein, we performed differential expression analysis. To identify the RNA targets of NONO in neuroblastoma, we carried out PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using an antibody recognising NONO protein. In the NONO knockdown experiment, four siRNA controls were sequenced and compared to eight NONO knockdown samples (two sets of four samples each using a distinct NONO siRNA). In the PARCLIP experiment (a separate sequencing run), one sample in each of KELLY, BEC2 and SKNAS cell lines was cross-linked and the PAR-CLIP protocol performed before sequencing. One sample cultured under normal conditions and without treatment was sequenced with the PAR-CLIP for each of the three cell lines.