GSM7184226: sgDDX3 arm, day 3 time point, replicate 2, RNAseq; Homo sapiens; RNA-Seq
See protocol from Calviello et al 2021 (PMID: 33905506). Briefly, Direct-zol RNA Miniprep (Zymo Research) kits were used to isolate RNA from either cytosolic cell lysate (lysed in (20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2 1% (v/v) Triton X-100, 25 U/ml TurboDNase (Ambion)) or cycloheximide-fixed ribosomes (treated with RNAseI (ambion) and isolated from Illustra MicroSpin Columns S-400HR). RNAseq libraries were prepared as per manufacturer's instructions using the NEBNext rRNA Depletion Kit V2 (NEB cat: E7400) and the NEBnext Ultra II Directional RNA Library Prep Kit (NEB cat: E7760). Ribosome Profiling libraries were prepared as previously described (PMID: 33905506). Briefly, purified RNA was ligated to 3' and 5' adapters, reverse transcribed, and PCR amplified.