GSM6519815: NPCs D868N Hi-C #3; Homo sapiens; Hi-C
For in situ Hi-C libraries preparation 5 milions of either NPCs or neurons were used. An already published experimental protocol was used 4. The procedures consist in different experimental steps: (i) crosslinking cells with formaldehyde at 1% concentration, (ii) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnI) within intact permeabilized nuclei, (iii) filling in and biotinylating the resulting 5′-overhangs, (iv) ligating the blunt ends, (v) shearing the DNA, (vi) pulling down the biotinylated ligation junctions with streptavidin beads, and (vii) analyzing these fragments using paired end sequencing. A first sequencing run of 5 milion reads perform to verify the experimental quality. After passing the quality check, sample were sequenced paired end on Nova-seq6000 at San Raffaele hospital omics facility. TruSeq