GSM9682228: CG8-A-Untreated; Homo sapiens; RNA-Seq
RNA was extracted with TRIzol reagent as per manufacturer's instructions (Invitrogen 15596062). The quality of isolated RNA samples was assessed using Agilent HS RNA ScreenTape (Agilent, 5067-5579) on the Agilent 4200 TapeStation. To obtain full-length transcriptomic data from cultured cells we performed SmartSeq2-based bulk RNA sequencing. In brief, RNA lysate clean-up was performed with Agencourt RNAClean XP Beads (Beckman Coulter, A639867). Next, Maxima H minus reverse Transcriptase (Thermo Fisher Scientific, EP0753) was used for reverse transcription and KAPA HotStart HIFI PCR ReadyMix (KAPA Biosystems, KK2602) was used for whole-transcription amplification (WTA). WTA products were purified with Ampure XP DNA SPRI beads (Beckman Coulter, A63881) and quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851). Quality was assessed with D5000 HS ScreenTape (Agilent, 5067-5588) on an Agilent 2200 TapeStation. WTA products were diluted for tagmention and indexing with the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) and two subsequent clean-ups with Ampure XP DNA SPRI beads. For quality control, Qubit dsDNA HS Assay Kit and Agilent D1000 ScreenTape (Agilent, 5067-5584) were used to determine concentration and size.  Samples were pooled together and sequenced on a NextSeq 2000 (Illumina) using a P2 flow cell and the following read configuration: R1, R2 = 38bp, I1, I2 = 8bp.