GSM8531063: APA-mut HepG2 cells, ethanol control, replicate 2; Homo sapiens; RNA-Seq
Total RNA was extracted using Trizol (Thermo Fisher) according to manufacturer's recommendations for adherent cell lines using Phaselock columns (Quantabio) prior to RNA purification with RNA clean up columns (NEB). Genomic DNA was removed using TURBO DNase (Fisher Scientific) according to the given protocol. RNA was quantified via NanoDrop (Thermo Scientific ND-8000) and quality checked by RNA Screentape on a Tapestation 4150 (Agilent). RNA samples were prepared using the QuantSeq 3' mRNA REV Library Prep Kit V2 (Lexogen), which captures polyadenylated RNA. Quality assurance for loading samples for sequencing was performed using a Qubit dsDNA High Sensitivity Assay (Thermo Scientific) on a Qubit 4 fluorometer (Thermo Scientific), and a High Sensitivity D1000 Screentape (Agilent) on a Tapestation 4150 (Agilent). The Lexogen QuantSeq samples were sequenced on a NovaSeq 6000 (Illumina) using a 2x100 cycle cartridge. A custom sequence primer was used for Read 1 according to instructions from Lexogen and Illumina.