3D interaction maps in wild-type and histone variant deletion mutants generated by chromosome conformation capture [Hi-C II]

Interaction matrices were generated by applying in situ Hi-C to wild-type and deletion mutant trypanosomes. DNA-DNA interactions were captured in situ in Trypansoma brucei nuclei, digested with MboI and re-ligated to obtain chimeric DNA molecules of previously interacting chromatin. The ligation products were purified and prepared for paired-end Illumina sequencing. Experiments were performed in duplicates for both the wild-type and the deletion mutant.