we used three sets of regulatory regions to perform motif enrichment of known TF families compared to the genome background. The regulatory regions included: (1) all differentially enriched EVT cell ATAC-Seq peaks based on estimated TF binding affinity, (...
(B–E) Native biotin ChIP-qPCR analysis of Hoxc6 peak primer set 22 (B), Pou5f1 peak primer set 9 (C), Pou5f1 peak primer set 22 (D), and Pou5f1 peak primer set 45 (E) in cells treated (green) or not treated (black) with aphidicolin following biotin enrichment during G1 syn...
ChIP experiments were carried out on infected HepG2-NTCP 8 days post infection with the ChIP-IT High sensitivity kit (Active motif, 53040) with minor modifications. Cells were fixed with 1% formaldehyde for 15 min at room temperature (RT) and quenched with 0.125 M glycine for 5 min...
To identify Brd4 binding regions, we used ‘SICER’ method with a window size of 50 bp and a gap size of 50 bp40. To eliminate non-specific binding of Brd4 antibody, we compared Brd4 ChIP-Seq data fromBrd4KO cells with that from two biological replicates of control (Pparγf/f) c...
We first determined the best suitable normalization control among Input, IgG, and mutant ChIP libraries (Fig. 1a; Supplementary Table 1). The peaks obtained by using the ChIP-seq reads of wild type against those of the cognate mutant showed the highest motif enrichment, compared with the ones...
To evaluate whether AGO2 might control chromatin binding for either protein, we performed differential ChIP-seq analysis of NELF-E and CDK9 upon depletion of AGO2. Interestingly, we found that depletion of AGO2 results in increased NELF-E binding at 249 genes and decreased binding at 138 genes...