Analysis of nucleus and cytoplasm-specific HNRNPK binding on SINEUP RNA by seCLIP

To check the subcellular location-specific HNRNPK binding sites on mouse SINEB2 repeat element, we prepared seCLIP (single-end enhanced crosslinking and immunoprecipitation assay) libraries from SINEUP-GFP transfected nuclear and cytoplasmic fractions from HEK293T/17 cells. Overall design: HEK293T/17 cells were co-transfected with SINEUP-GFP and pEGFP-C2 plasmids, crosslinked by UV, and separated into nuclear and cytoplasmic fractions. Both fractions were immunoprecipitated with anti-hnRNPK antibody (IP sample) and corresponding samples without immunoprecipitation were used as input control and seCLIP libraries were prepared. Two biological replicates each for cytoplasmic IP/input, and nuclear IP/input. Update: [09-15-2023] Read strand information corrected in the cyt.e.peaks.norm.bed, cyt.e.peaks.norm.full.bed, nuc.e.peaks.norm.bed, and nuc.e.peaks.norm.full.bed files.