SRX1307060 BE4 SRP015821 phs000536 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. SRS1100658 BE4 BE4 AMPLICON GENOMIC PCR 100 0 Application Read Forward 1 Illumina HiSeq 2500 alignment_software Bowtie2 SRX1307061 Barretts_Meltzer SRP015821 phs000536 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. SRS1100659 Barretts_Meltzer Barretts_Meltzer AMPLICON GENOMIC PCR 100 0 Application Read Forward 1 Illumina HiSeq 2500 alignment_software Bowtie2 SRX1307062 NORMAL_ES_2 SRP015821 phs000536 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. SRS1100660 NORMAL_ES_2 NORMAL_ES_2 AMPLICON GENOMIC PCR 100 0 Application Read Forward 1 Illumina HiSeq 2500 alignment_software Bowtie2 SRX1307063 Normal_BE4 SRP015821 phs000536 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. SRS1100657 Normal_BE4 Normal_BE4 AMPLICON GENOMIC PCR 100 0 Application Read Forward 1 Illumina HiSeq 2500 alignment_software Bowtie2 SRX1307064 Normal_Meltzer SRP015821 phs000536 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. SRS1100656 Normal_Meltzer Normal_Meltzer AMPLICON GENOMIC PCR 100 0 Application Read Forward 1 Illumina HiSeq 2500 alignment_software Bowtie2 SRX1307065 TUMOR_ES_2 SRP015821 phs000536 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. SRS1100654 TUMOR_ES_2 TUMOR_ES_2 AMPLICON GENOMIC PCR 100 0 Application Read Forward 1 Illumina HiSeq 2500 alignment_software Bowtie2 SRX1307066 Tumor_Meltzer SRP015821 phs000536 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. SRS1100655 Tumor_Meltzer Tumor_Meltzer AMPLICON GENOMIC PCR 100 0 Application Read Forward 1 Illumina HiSeq 2500 alignment_software Bowtie2