SBCapSeq Protocol manuscript files for 'Quantifying tumor heterogeneity, clonal dynamics, and cancer driver gene evolution from Sleeping Beauty transposon mutagenesis models using SBCapSeq'
Supplementary datasets and other information accompanying manuscript: Quantifying tumor heterogeneity, clonal dynamics, and cancer driver gene evolution from Sleeping Beauty transposon mutagenesis models using SBCapSeq by Karen M. Mann Ana M. Contreras-Sandoval, Liliana Guzman-Rojas, Justin Y. Newberg, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Neal G. Copeland, Nancy A. Jenkins, and Michael B. Mann.
SBCapSeq is a transposon-based liquid-phase capture experimental and bioinformatic workflow optimized for Ion Torrent sequencing. SBCaptureSeq permits selective, semi-quantitative, and scalable deep sequencing of Sleeping Beauty transposon insertion sites from adaptor-ligated, barcoded Ion Torrent libraries created from populations of cells (bulk specimens) and single cells from both tumor and non-tumor genomes. This protocol includes detailed procedures for genomic DNA isolation, library preparation, capture hybridization, target sequence enrichment, sequencing, and data analysis. The SBCapSeq method, which takes about 7–10 days to perform, permits semi-quantitative sequencing and has been specifically optimized for Sleeping Beauty transposon mutagenesis genetic studies.