RNA-Seq of cell lines: with and without Ribonuclease R
First, ribosomal RNA (rRNA) was removed with the NEBNext rRNA Depletion Kit. Next, Ribonuclease R (RNAse R) treatment was performed according to our previously described protocol (Vromman et al. 2021). In summary, one sample of each cell line was treated with RNase R and one sample of each cell line was treated as a buffer-control. This was followed by a clean-up step using Vivacon 500, 10,000 MWCO Hydrosart columns. Next, the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used in combination with the NEBNext Multiplex Oligos for Illumina to index and prep the samples