GSM6742180: TDP2–/– + Mock, 6 h, replicate 3; Homo sapiens; OTHER
RNA was extracted as described previously (Hirabayashi et al.,PMID: 31477927).Briefly, fresh cells were lysed in the presence of α-amanitin, and the nuclear insoluble fraction was isolated. Following DNase treatment, RNA was purified using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions. NET-CAGE library preparation, sequencing, mapping, and gene expression analysis were performed by DNAFORM (Kanagawa, Japan). In brief, the cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5′ cap structures of RNAs were oxidized and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both cDNA ends, double-stranded cDNA libraries (CAGE libraries) were constructed.