Identification of cis elements for temporal and spatial control of DNA replication

This SuperSeries is composed of the SubSeries listed below. Refer to individual Series The GSE114139_ERCEs_predicted_mm10.txt file was created using all of the data from the series of experiments that are part of Superseries GSE114139. For genome-wide prediction of ERCEs, CTCF-independent Hi-C interactions (20kb resolution, FDR 5%) were retrieved using the auxin-induced CTCF depletion HiC (Nora et al., 2017) with Fit-Hi-C program (Ay et al., 2014). The significant interactions were then filtered based on their overlap with P300-binding sites, non-lamin-associated domains and Oct4, Sox2 and Nanog (OSN) triple peaks on both sides of the interaction. The final set of interactions were then flattened into 1D regions, which were further processed to merge multiple sites as the predicted ERCEs.