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Table 1 DNAse Hi-C protocols used in this study

From: A cookbook for DNase Hi-C

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