title: GSM2458211: WT 0h LPS 100U DNase rep2; Mus musculus; DNase-Hypersensitivity
library_construction_protocol: After treatment with 10 ng/ml LPS for the indicated times, cells were pelleted at 500 g for 5 min at 4°C followed by nuclei isolation with ice-cold buffer A (15 mM Tris-Cl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (pH 8), 0.5 mM EGTA (pH 8), 0.04% NP-40, 0.5 mM Spermidine), and the nuclei were centrifuged at 500 g for 5 min at 4°C. The isolated nuclei were washed with fresh-cold buffer A and chromatin from 5 million cells were digested with 80 U/ml DNase I (Sigma) for 3 min at 37ºC followed by termination of the reaction with an equal volume of Stop buffer (50 mM Tris-Cl, pH 8, 100 mM NaCl, 0.1% SDS, 100 mM EDTA, pH 8). The DNase I digested nuclei were deproteinized at 55ºC overnight with 10 μg/ml of RNaseA (Invitrogen) and Proteinase K (Ambion). Digested DNA fragments were purified using phenol-chloroform and enriched by size selection over a sucrose gradient. DNA fragments between 100 bp and 500 bp were precipitated and dissolved in nuclease free water (Ambion). Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.
attributes.tag: GEO Accession
attributes.value: GSM2458211