title: GSM6722713: Hi-C in E13.5 XY supporting cells rep1; Mus musculus; Hi-C
library_construction_protocol: Fixed nuclei were extracted adding ice-cold custom-made lysis buffer containing the following components: 50mM Tris HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton X-100, 25X Protease Inhibitor in MilliQ water. Extracted nuclei were then collected, snap frozen and stored at -80 °C or further processed with the following steps: digestion with Mbo I RE, re-ligation of the digested fragments, de-crosslinking and DNA purification. The Hi-C library was sheared using Covaris sonicator and the following parameters: 2 cycles, each 50'', 10% duty, 4 intensity, 200 cycles/burst, temperature: 4°C. Sheared sample was then treated following the NEBNext Ultra DNA Library Prep kit for Illumina guidelines (end repair, dA-tailing, adaptor ligation, PCR enrichment of Adaptor ligated DNA, DNA purification).