ChIP-Atlas: SRX475802

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: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: ChIP for Atf3 was performed using the EZ-Magna ChIP G Kit (Millipore) according to the manufacturer's instructions. In brief, three biological replicates of BMDMs from WT and Atf3-deficient mice were treated with HDL, CpG, HDL then CpG or left untreated. Cells were then cross-linked with 1% paraformaldehyde, before they were lysed and chromatin was sheared by sonication for 30 min with the Covaris S220. Immunoprecipitation was performed over night at 4 °C using 2.5 μg of rabbit polyclonal anti-Atf3 antibody (C-19X, Santa Cruz). After washing, eluted samples were reverse cross-linked and treated with RNase A and proteinase K per the manufacturer's recommendations. ChIP fragments were ligated to NEXTflex ChIP-Seq barcode adaptors using the NEXTflex ChIP-Seq Kit (both BioO Scientific). Adaptor ligated DNA fragments were size-selected (150–250 bp), PCR-amplified, further size selected (150–250 bp), pooled and sequenced on an Illumina HiSeq-1000 sequencer according to the manufacturer's instructions.