Illumina HiSeq 2000 sequencing; DNase-Hypersensitivity_Diffuse large B cell lymphoma GCB_
design_description
Karpas nuclei were isolated and briefly treated with different concentrations of DNaseI enzyme. Based on quality check 80U DNase treated sample was further processed with sucrose fractionation and purified sample was passed to the illumina library prep
EXPERIMENT_TYPE
Chromatin Accessibility
EXTRACTION_PROTOCOL
Nuclei were isolated from respective cells using Buffer A (15mM NaCl,60mM KCl,1mM EDTA, pH 8.0,0.5mM EGTA, pH 8.0,15mM Tris-HCl, pH 8.0,0.5mM Spermidine ) supplemented with 0.015% IGEPAL CA-630 detergent.
DNASE_PROTOCOL
DNaseI treatment was done for 3 minutes and reaction was stopped with stop buffer ( 50mM Tris-HCl, pH 8, 100mM NaCl, 0.10% SDS, 100mM EDTA, pH 8.0, 1mM Spermidine, 0.3mM Spermine), sample was further fractionated on 9% Sucrose gradient for  24hrs/25000rpm at 16ºC.
LIBRARY_GENERATION_FRAGMENT_SIZE_RANGE
149