GSM7729634: 317E cell line NUT  rep 1; Mus musculus; OTHER
Cells were fixed with 0.1% formaldehyde for 1 minute. Tissue was fixed with 0.2% formaldehyde for 2 minutes. Cells were bound to Con-A beads and incubated overnight with target antibodies. Bead bound cells were washed and incubated with pAG-MNase for 60 minutes at 4degC before being washed and incubated with CaCl2 to activate MNase. Reaction was stopped with EGTA,EDTA containing buffer and incubated for 10minutes at 37degC to release DNA. SDS and proteinase K were added to each sample before overnight incubation at 55degC to reverse cross link. DNA was purified using oligo clean and concentrator. Yields were determined using Qubit 2.0 Fluorometer with 1x dsDNA HS assay kit Immunoprecipitated DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality was assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep kit with PCR (Roche, Basel, Switzerland) per manufacturer's recommendations. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied systems, California, USA). Illumina® 8-nt unique dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus 10B (Illumina, California, USA) with a read length configuration of 150 PE for 8M PE reads (4M in each direction).