Amplification of genomic DNA junctions was performed by linear amplification-mediated PCR, and bioinformatic analysis of integration sites was performed as described previously.10 (link)
To analyze the sequencing data, sample-specific barcoded sequencing reads were demultiplexed using CASAVA, an Illumina software package. The quality of sequencing runs of resulting fastq files was evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ). Reads starting with the barcode 5′-GTATGTAAACTTCCGACTTCAACTG-3′ that follows the TA dinucleotide, which is characteristic of SB integration, were aligned against the latest version of mouse reference genome (GRCm38/mm10 [December 2011]) using Bowtie2.49 (link) Only reads that mapped exactly to a unique position in the reference genome were kept for further analysis. To analyze the distribution integrations, annotations of exons, and coding DNA sequence (CDS) of the corresponding reference, genome were downloaded and the percentage of integration sites overlapping with the given genomic coordinates was analyzed using BEDTools.50 (link) We have indexed and created 142 normal, shuffled, and randomized windows of mouse genome and counted the number of integrations for each window and plotted the density.
To analyze the sequencing data, sample-specific barcoded sequencing reads were demultiplexed using CASAVA, an Illumina software package. The quality of sequencing runs of resulting fastq files was evaluated using FastQC (
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