Integration assay. Assays were monitored as described (doi: 10.1038/ng.3866). Briefly, two kinds of G401 cells were used. Cells G401-shPGBD5 expressing a shRNA directed against the share regions of PGBD5 mRNA isoforms. In those cells, the PGBD5 expression, Hs524, was shown to be off (doi: 10.1038/ng.3866). Cells G401-shGFP expressing a shRNA directed against the GFP. These cells expressed PGBD5 while G401-shPGBD5 cells were used as negative controls. Each sample of 100,000 cells in a well of a 24-well plates of plaque assays was co-transfected with 500 ng DNA plasmid donor of NeoR cassette included within a transposon. Two days post-transfection, each cell sample was transferred in a cell culture dish (100 mm diameter) and selected with a culture medium containing 2 mg/mL G418 sulfate (Eurobio Scientific, Les Ulis) for 15 days. After two washing with 1X saline phosphate buffer, about 1,600 cell clones were harvested for genomic DNA preparation using the DNeasy kit (Qiagen, Hilden, Germany). Linear amplification-mediated PCR (LAM-PCR) were performed to amplify the vector-genomic DNA junctions of piggybac and Tcr-pble vectors as described (doi: 10.1007/978-1-61779-603-6_15). All PCR were done using the high fidelity Q5 DNA Polymerase (New England Biolabs, Ipswich, MA). Final PCR products were purified, quantified and gathered in equimolar DNA amounts for each transposon vector (4 populations of LAM-PCR products) before to be used to make Illumina libraries using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext Multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA). Fragment size selection, library quality control and Illumina sequencing (MiSeq 250 nucleotides, TruSeq SBS Kit v3) were achieved at the Plateforme de Séquençage Haut Débit I2BC (Gif-sur-Yvette, France). DNA quantities were monitored at various steps in the procedure with the Qubit® dsDNA (Molecular Probes, Eugene, USA).
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