title: GSM5899807: B6-2; Mus musculus; Hi-C
library_construction_protocol: The nuclei were first extracted by lysing the cells with cell lysis buffer as before. The extracted nuclei were then subjected to HindIII digestion followed by proximity ligation with T4 DNA ligase to create spatial ligates. After proximity ligation, the DNA was extracted and prepared for the secondary restriction enzyme (DpnII) digestion. All DNA obtained was subjected to DpnII cutting before being self-ligated to form self- circes. The unligated DNA was then removed using Lambda exonuclease. The self-circles were re-linearized by digesting again with HindIII. All DNA recovered was applied to generate the sequenceable libraries using the Illumina Truseq platform. Briefly, fragment ends were first repaired with the DNA end-repair enzyme cocktail. Then, a base “A” was added to each end by Klenow fragment (NEB, M0212) before ligated to a modified Truseq adapter using Quick ligase (NEB, M0202). We used the regular i7 indexes as sample index and i5 as fragment index by changing it to random indexes (i5: NNNNNN).