GSM7950009: HEK293T cells, Parental, rep 3; Homo sapiens; RNA-Seq
RNA for CAG containingreporter cell lines was extracted using Aurum total RNA mini kit (BioRad) withon-column DNase treatment, following themanufacturer's protocol. The Qubit RNA high sensitivity assay wasused to obtain RNA concentrations(Thermo Fisher Scientific). RNA quality waschecked via capillary electrophoresis on a 5300 fragment analyzer (AgilentBioanalyzer) using the RNA AnalysisDNF-471 RNA kit (Agilent). The NEBNext Ultra IIDirectional RNA Library Prep Kit (Illumina) with NEBNext rRNA Depletion Kit(New EnglandBiolabs) was used to prepare RNA-seq libraries, with a total of500 ng input RNA from each sample. The manufacturer'sprotocols were followed,with the following exceptions: 40× adaptor dilutions were used, and 13 cyclesof libraryamplification were performed. The resulting libraries were pooled inequimolar amounts, quantified using the NEBNextLibrary Quant Kit for Illumina(New England Biolabs), quality checked via capillary electrophoresis on the5300fragment analyzer (Agilent Bioanalzyer) using the DNF-474 HS NGS kit(Agilent). Libraries with sufficient quantitywere sequenced using paired-end, 75 base pairsequencing (parental and clone 37), or 100 base pair sequencing (clone 15) onthe Illumina NextSeq 500 sequencer at the University at AlbanyCenter for functional genomics. All datasets had total read depths greaterthan 40 million reads.