Northern Blot Analysis of RNA

Northern blot analysis was carried out as previously described (Andreassen et al., 2018 (link)). Briefly, 10 μg of RNA was run on a denaturing 8% polyacrylamide gel for 2 h at 300 V. Separated RNA was blotted onto a Zeta-probe nylon membrane (Bio Rad) using a semi-dry transfer unit for 1 h at 400 mA. RNA was cross-linked to the membrane with UV radiation. Oligonucleotide probes (see Supplementary material; Supplementary Table S1) were 5′-labeled with³² P-ATP using T4-polynucleotide kinase (New England Biolabs). Membranes were pre-hybridized for 10 min at 42°C before probing with 5′-labeled oligos overnight. Probed membranes were washed once in 2× SCC and 0.1% SDS for 10 min followed by a 10 min wash in 0.5× SCC and 0.1% SDS. Probed membranes were visualized by phosphorimaging on a Typhoon scanner (GE Healthcare).