Fig. 1

Transposon Insertion Profiling by sequencing (TIPseq) workflow. High molecular weight genomic DNA was extracted from primary and secondary glioblastoma (GBM) tumors, oncosphere cultures expanded from primary GBM, and matched blood samples from the same patients. Genomic DNA was then digested in six parallel reactions each using one of a panel of restriction enzymes. In the diagram, LINE-1 insertions are depicted as orange segments of the genomic DNA; restriction enzyme cuts sites are illustrated with different symbols. Vectorette oligonucleotides designed to match each restriction enzyme sticky end were ligated to the DNA fragments, and the 3′ ends of LINE-1 sequences and downstream DNA were amplified. Genomic DNA fragments without binding sites for the LINE-1 amplification primer are not enriched in this PCR. Amplified DNA was then randomly sheared and prepared for Illumina sequencing