title: HiC of S. pneumoniae; delta-SMC
design: Cells were pre-grown until OD600 = 0.3 in C+Y medium at 37 C in presence of the inducer (aTc) for HU-depletion strain (VL5898). Cells were then washed three times with CY and diluted 15 times in 10 ml of fresh C+Y medium supplemented with or without the inducer and let grow for three hours up to OD600 = 0.1 - 0.2. Cell fixation was performed with 3% formaldehyde (Sigma-Aldrich, cat. no. F8775). Quenching of formaldehyde with 300 mM glycine was performed at room temperature for 20 min under gentle agitation. The samples were recovered by centrifugation (4000 g, 10 min, 4 C), washed with 10 mL 1X PBS, re-centrifuged, and stored at  80 C until processing. Hi-C experiments were performed as described in ref. (Cockram, Thierry, and Koszul 2021), as well as DNA extraction, purification, and processing into a sequencing library. Proximity ligation libraries were sequenced using pair-end (PE) Illumina sequencing (2  35 bp, NextSeq500 apparatus) at the sequencing platform of the Institut Pasteur of Paris.
identifiers.namespace: SUB14752130
identifiers.id: AT736_D39V