GSM8539299: SW480, Fedratinib, 2 hour, biological replicate 2; Homo sapiens; OTHER
Cells were lysed directly in TRIzol followed by isolation of total RNA.The isolated total RNA was further treated with DNAse (TURBO DNA-free Kit; Invitrogen) and a spike-in cocktail of Bru-labeled and unlabeled RNA was mixed in with total RNA. Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences). Strand-specific libraries were prepared from a modified protocol as described previously (McShane et al., bioRxiv, 2024). Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first-strand synthesis. A universal ligation adapter and dual-index, barcoded primers for were used for PCR in the preparation of these libraries. Size selection for all libraries was performed via agarose gel excision.