Capture-C of human: siControl differentiated HUDEP-1 cells
Capture-C assay was carried out using the in-situ method as described before with minor modifications. One million cells were used for each reaction. In brief, after fixation with 1% formaldehyde, cells were digested overnight at 37 C using MboI (NEB, Cat. #R0147). Proximity ligation was carried out overnight at 25 C with T4 DNA Ligase (NEB, Cat. # M0202M). After reverse-crosslinking, DNA was purified and sheared to 300-500bp fragments using Covaris M220 sonicator, and then library preparation was performed using the DNA library preparation kit (Vazyme, Cat.# ND607) as per the manufacturers protocol. Two micrograms indexed and mixed library was use as input for the two rounds downstream hybridization and biotin capture with biotin labeled oligo (Supplementary Table) following with manufactures recommendation (Genscript, NGS09612).Two biological replicates per condition were sequenced.