CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing

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Discordant read pairs and sequences. All discordant read pairs for ST77 and the position of the start of the read are shown, as well as their mated sequence and pair relationship. Integration of Agrobacterium tumefaciens transfer DNA (T-DNA) involves rearrangements of target plant DNA sequences Integration of T-DNA binary vector ‘backbone’ sequences into the tobacco genome: evidence for multiple complex patterns of integration Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions Assessment of pleiotropic transcriptome perturbations in Arabidopsis engineered for indirect insect defence New insights into an old story: Agrobacterium-induced tumour formation in plants by plant transformation Identification of transferred DNA insertions within Arabidopsis genes involved in signal transduction and ion transport Determination of gene copy number and genotype of transgenic Arabidopsis thaliana by competitive PCR Identification of transgene integration loci of different highly expressing recombinant CHO cell lines by FISH The use of combined FISH/GISH in conjunction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco A genome walking strategy for the identification of eukaryotic nucleotide sequences adjacent to known regions Next-generation genome sequencing can be used to rapidly characterise sequences flanking T-DNA insertions in random insertional mutants of Leptosphaeria maculans Identification of the genomic insertion site of Pmel-1 TCR alpha and beta transgenes by next-generation sequencing Time- and cost-efficient identification of T-DNA insertion sites through targeted genomic sequencing The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data Molecular characterization of transgene integration by next-generation sequencing in transgenic cattle Recombinant expression of homodimeric 660 kDa human thyroglobulin in soybean seeds: an alternative source of human thyroglobulin The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets Soybean-derived thyroglobulin as an analyte specific reagent for in vitro diagnostic tests and devices Sublethal staphylococcal enterotoxin B challenge model in pigs to evaluate protection following immunization with a soybean-derived vaccine T-DNA vector backbone sequences are frequently integrated into the genome of transgenic plants obtained by Agrobacterium-mediated transformation Source.

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