CapSeq of SK-N-BE(2)C nuclear RNA
Nuclear RNA from SK-N-BE(2)C cells (untreated or treated with 80 mM KCl for 1h) was fractionated to 90-250 nt, size extracted, and capped fragments were isolated by pulldown with eIF-4E cap binding protein and subjected to phosphatase and decapping as described (Xie, M., Li, M., Vilborg, A., Lee, N., Shu, M.D., Yartseva, V., Sestan, N., and Steitz, J.A. (2013). Mammalian 5'-capped microRNA precursors that generate a single microRNA. Cell 155, 1568-1580.). The resulting purified capped fragments were used for library preps according to protocols for small RNA library preps and sequenced using single-end 75 bp sequencing.