title: Hi-C from mouse embryonic stem cell derived neural stem cells
design: Hi-C from mouse embryonic stem cell derived neural stem cells
library_construction_protocol: Cells were detached with Accutase, counted and crosslinked with 1% (final) formaldehyde in their medium. The reaction was quenched with 0.125M (final) glycine, and cell pellets were washed with PBS, snap-frozen, and stored in a -80 freezer. The pellet of 5 million cells was used for each Hi-C experiment.  NS cells were grown on laminin-coated plates in neural differentiation medium containing N2 and B27 supplements along with recombinant murine EGF and bFGF to a final concentration of 10 ng/ml. Cells were split at 80% confluence with a density of 35000 cells/sq.cm. The medium was exchanged daily.  Ddx5 depletion was carried out in Ddx5-FKBP NS Cells by treating with 500nM of dTAG13 dissolved in culture media for 24h Hi-C experiments were performed as described as describer before (Rao et al., 2014) Hi-C libraries were generated using NEBNext Ultra II DNA Library Kit, according to manufacturer's instructions