Chromatin accessibility to investigate the TF-chromatin information patterns encoded in the accessible genome

Purpose: The goal of this study is to use chromatin accessibility data to study the information patterns of chromatin accessibility that encode TF-chromatin interactions. Methods: We generated chromatin accessibility data from the GM12878 lymphoblastoid cell line using a modified protocol where the ATAC-seq fragments are sonicated during the library preparation. The goal of the sonication step is to disrupt the observed fragment size distribution, therefore masking local TF-chromatin interactions encoded in the larger fragment sizes (e.g. nucleosome phasing) without affecting the levels of chromatin accessibility. We generated ATAC-seq libraries of the GM1287 lymphoblastoid cell line under two conditions: with and without a sonication step to disrupt the ATAC-seq fragment size distribution.