BCBL1-1TREX-RTA-Luc in the absence of rapamycin. These samples were used in Gene Expression analyses. This clone was used as biological replicate 3
Library preparation for poly(A) RNA was performed according to Ion Total RNA-Seq Kit v2, whole transcriptome RNA protocol (ThermoFisher Scientific, Publication #MAN0010654 Revision B.0) with the exception of: purification of fragmented RNA and purification of cDNA was with 1.8x Agencourt RNAClean XP beads (Beckman Coulter, Inc.) (Ovation Universal RNA-Seq System User Guide, NuGEN) and an additional Agencourt AMPure XP 1.0x bead (Beckman Coulter, Inc.) cleanup of the finished library. Libraries were quality-controlled and quantified using Agilent Bioanalyzer 2100 High Sensitivity DNA Assay (Agilent Technologies) and Qubit dsDNA HS (High Sensitivity) Assay (ThermoFisher Scientific). 50pM of library was templated on the Ion Torrent Chef for 200bp and sequenced on the Ion Torrent S5 using a 540 chip.