This composite track displays normalized ATAC-seq data used as input for UniversalEPI to predict Hi-C interactions. The data is derived from ENCODE cell lines and primary cells, providing a comprehensive view of chromatin accessibility across various cell types.
The ATAC-seq data in this track hub has been normalized using EdgeR's Trimmed Mean of M-values (TMM) normalization method, with the GM12878 cell line as the reference. This normalization ensures that the chromatin accessibility profiles are comparable across different cell types, accounting for differences in sequencing depth and library composition. Each track represents a specific cell line or primary cell type, allowing users to explore cell-type-specific accessibility patterns.
These tracks are intended for researchers studying chromatin accessibility and its relationship to gene regulation and 3D genome organization. They serve as the input data for the UniversalEPI model, which predicts Hi-C interactions (see the companion UniversalEPI Hi-C Predictions composite track). Users can toggle individual tracks to compare accessibility profiles across cell types or overlay them with other genomic features in the UCSC Genome Browser.
For questions or feedback about this track hub, please contact Prof. Dr. Valentina Boeva.