title: GSM5467943: Ribosome profiling in Nrde2 knockout mES cells_ replicate 2; Mus musculus; OTHER
library_construction_protocol: Cells were lysed and digested with Benzonase. Ribosome footprints were isolated as a band migrating slightly slower than a 35 nt ssDNA oligo on a 15 % Novex TBE-Urea polyacrylamide gel. After ribosomal RNA depletion, ribosome footprints were polyadenylated and purified using SPRI beads. For details see Flemr et al, 2021. RNA was reverse transcribed with SuperScript II (ThermoFisher 18064014) in the presence of a template-switching oligo. The resulting cDNA was purified with SPRI beads and libraries were amplified using NEBNext Ultra II Q5 master mix (NEB M0544L). For a detailed protocol, see Flemr et al, 2021. BCLIP-seq