One shot top10 electrocomp e coli cells

Filled site PCR products were cloned for sequencing in a TOPO XL PCR cloning kit (Life Technologies) using One Shot TOP10 Electrocomp E. coli cells (Invitrogen). Empty site and L1-genome junction amplicons were cloned using the pGEM-T Easy Vector System (Promega). DNA was obtained from clones using a QIAPrep Miniprep kit (QIAGEN). Filled site PCR products were also directly sequenced, with DNA concentration quantified using a Qubit dsDNA HS Assay kit. For filled site PCR products, stepping primers (Table S4) along the L1 sequence were used for independent capillary reactions covering the whole length of the amplicon/insert. To estimate the lengths of polyA tracts found in the 3ʹ L1-genome junctions of the CTRL-36 heterozygous germline L1 insertions and the somatic L1 insertion, we capillary sequenced at least 3 clones obtained from PCRs using DNA extracted from liver tissue (germline L1s) or each MDA-amplified neuron (somatic L1s). Capillary sequencing was performed by Macrogen (South Korea) and the Australian Genome Research Facility (AGRF, University of Queensland, Australia).