ChIP-seq study on Dnd proteins

Tto get the DNA PT modification proteins binding regions on the genome, ChIP with anti-Flag antibody followed by Illumina sequencing was applied. Overall design: We performed six ChIP experiments, including three biology replicates of Flag-DndC in YF11 (S. enterica 87?dndC mutant), three different strains expressing DndBCDE in WXL1 (S. enterica 87?dndBCDE mutant) with Flag tag fused to DndC, DndD, and DndE respectively (Supplementary Fig. 1a), and reproducible patterns were identified in all six ChIPs . For each ChIP, three negative controls were performed: the same strain without antibody control, Dnd protein without Flag tag control, and Flag tag not fused to Dnd protein control.