GSM3265176: VL3-3M2 WT DamID; Mus musculus; OTHER
Genomic DNA was harvested from VL3-3M2 cells transduced with either unfused Dam or Dam-Lamin B1 retroviruses. DamID enrichment was performed as described in Vogel et al., 2007. 1-2 μg DamID material was subjected to end repair using the NEBNext End Repair Module (New England Biolabs) and cleaned up using DNA Clean and Concentrator -5 (Zymo Research). Cleaned up DNA was ligated with 5U T4 DNA ligase (Roche) per 1 μg material in 20 μL to generate a library of large DNA fragments. This DNA library was diluted to 200 μL in H2O, sonicated for one hour in 1.5 mL in DNA LoBind tubes (Eppendorf) using a Bioruptor (Diagenode), then transferred to 1.5 mL TPX tubes (Diagenode) for four rounds of 10 min sonication to yield fragments of 150-300 bp in size. Samples were transferred to new TPX tubes between each round of sonication to minimize loss of DNA fragments. The sonicated DNA was transferred to 1.5mL DNA LoBind tubes, ethanol precipitated and resuspended in 10 μL of 10 mM Tris-HCl pH 8.0. Samples were quantified using Qubit and sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).