Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication

This data repository provides access to the LINE-1 (L1) insertion site data from Flasch, et al., 2019:
https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub

Please see file L1_actual_and_random_insertions_help.docx for more detailed information.

Files weighted_moel_142_102917_corrected.txt and weighted_model_142_102917_uncorrected.txt carry a list of all possible 7-mer insertion sites, one per row, with site weights calculated based on observed L1 insertion sites. The files are either corrected or uncorrected for the frequency of those sites as found in the human genome, respectively. A header line defines the columns.

The weight files described above were used to construct the simulated insertions sets described below.

Archive all_insertion_sets.tar contains a series of insertion files, each with the complete data set used to analyze insertions from the named cell line.

Column 5 is the iteration number, where:

iteration == 0 identifies the actual, observed insertions

each iteration > 0 identifies one round of simulation, up to 10K total simulations

each iteration has the same number of insertions

Column 4 is the insertion number within each actual or simulated insertion set.