title: L1 Retrotransposition evaluated by L1 seq in individuals with the precursor Barrett's esophagus which progressed to esophageal adenocarcinoma
design: DNA was isolated from the frozen tissue samples, from thinly sliced sections of tissue embedded in OTC freezing media with the DNeasy kit (Qiagen).  Our samples were not micro-dissected to remove all normal tissue largely because half of our samples were either acquired as genomic DNA or previously frozen tissues.  Equal amounts of genomic DNA from each individual were pooled by group.  Hemi-specific PCR amplified the young, active L1 elements from the genome (Ewing et al., 2010).  Products between 200 and 500 base pairs were excised and gel purified for continuing library prep.  Using Bowtie2, the alignments were sorted based on presence or absence of L1 sequence, and the reference insertions and previously published polymorphic insertions were identified (Ewing et al., 2010). Our bioinformatics analysis was essentially identical to previous analyses (Ewing et al., 2010). See Doucet-O'Hare et al., 2015 for more detail. 
attributes.tag: alignment_software
attributes.value: Bowtie2