Extended Data Fig. 9: Micro-C control experiments and optimization of MNase digestion.

a, Micro-C contact map for wild-type E. coli cells processed according to the standard Micro-C protocol, but without the addition of DNA ligase. b-d, Comparison of Micro-C contact maps for wild-type E. coli cells grown at 37 °C and fixed with formaldehyde at room temperature, as per the standard Micro-C protocol (b), those grown and fixed at room temperature (c), and those grown and fixed at 37 °C (d). e, In vivo protein-protein crosslinks induced by treatment of E. coli cells with DSG and DSS, assessed by mass spectrometry. Protein names are according to UniProt. f, Distribution of DNA between soluble (super) and insoluble (debris) fractions following treatment with increasing amounts of MNase of wild-type E. coli cells fixed with formaldehyde alone (upper gel) or with formaldehyde and DSG (lower gel). g, Gel shows a typical MNase titration experiment. An amount of 5 U was selected as optimal, producing the desired fragment sizes range. h, Gels show four different samples tested after MNase digestion and ligation for two biological replicates. Sample 4 (non-relevant to the present study) indicates over-digestion, leading to excessive fragmentation, in replicate 1. For uncropped gels, see Supplementary Fig. 1. i, Micro-C contact maps for replicate 1 and 2 of sample 4, demonstrating similarity between contact maps (stratum-adjusted correlation coefficient 0.978).