NextSeq 500 sequencing; Stable knockdown or over expression of the SPOP-substrate ZMYND11 in Y87C SPOP-mutant and control VCaP cells
For stable knockdown experiments, cells were infected with pLKO-1 vectors (Sigma). Two different hairpins were used. After infection, cells were selected in the presence of puromycin (2 ug/ml).  VCaP were grown in DMEM (Gibco) and supplemented with 10% FBS (Gibco), 1% Penicilin/Streptomycin/L-Glutamate. All cells were incubated at 37°C and 5% CO2. Cells were routinely tested for mycoplasma contamination. RNA was extracted using the Rnasy kit (Qiagen) and sample quality was assessed using Agilent Bioanalyzer. RNA libraries were prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®