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. 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.