ChIP-Atlas: SRX2491797

Antigen

Cell type Class: Blood
Cell type: Macrophages
MeSH Description: The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)

library_strategy: DNase-Hypersensitivity
library_source: GENOMIC
library_selection: DNase
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.