Table 1 DNAse Hi-C protocols used in this study
Protocol name | Short protocol description |
|---|---|
Ma et al. (reanalysed) | Data from Ma et al. [22] reanalysed using our pipeline |
Ramani et al. (reanalysed) | Data from Ramani et al. [21] reanalysed using our pipeline |
Protocol Ma et al. | Reproduction of the protocol from [22] in our laboratory |
Protocol Ma et al. new blunt | Modification of the protocol from [22]. We changed the blunt-adapter sequences to prevent the formation of adapter multimers |
Protocol Ma et al. long linker | Modification of the protocol from [22]. We abolished the two-step ligation procedure. We used the long linker derived from the BAT-Hi-C protocol instead |
Protocol Ramani et al | Reproduction of the protocol from [21] in our lab |
Protocol Ramani et al. long linker | Modification of the protocol from [21]. We abolished the two-step ligation procedure and used the long linker derived from the BAT-Hi-C protocol instead |
Protocol Ramani et al. biotin fill-in | Modification of the protocol from [21]. We abolished the two-step ligation procedure. End-labelling with biotinylated dCTP nucleotides was performed during the end-repair step following DNase treatment |