ChIP-Atlas: ERX711393

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.)

ENA first public: 2015-02-26
ENA last update: 2018-03-08
ENA-CHECKLIST: ERC000011
External Id: SAMEA3267658
INSDC center alias: MDC
INSDC center name: Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
INSDC first public: 2015-02-26T17:03:04Z
INSDC last update: 2018-03-08T23:43:41Z
INSDC status: public
Submitter Id: E-MTAB-3343:H3K4me3_M1_3
broker name: ArrayExpress
cell type: macrophage
common name: house mouse
sample name: E-MTAB-3343:H3K4me3_M1_3
sex: male
stimulus: 10ng/ml LPS 24h
strain: C57BL/6JOlaHsd

library_name: H3K4me3_M1_3
library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Primary bone-marrow-derived murine macrophages were grown in RPMI1640 (GIBCO) supplemented with 10% FCS, 10mM HEPES, 1% Penicillin-Streptomycin, 5µM beta-mercaptoethanol at a density of 40 million cells per 150cm(2) cell culture flask. After attachment for 2h cells were stimulated with 10ng/ml LPS (Sigma-Aldrich) [M(LPS)] for 24h. 40mM NaCl were added where applicable. 40 million macrophages per group were used to isolate nuclei by centrifugation through a dense sucrose cushion. Subsequently, samples were digested with micrococcal nuclease (Sigma-Aldrich) to generate native chromatin templates consisting mainly of mononucleosomes. Abundance of mononucleosomal DNA was confirmed by gel electrophoresis. Chromatin was extracted with RIPA buffer and cellular debris removed by centrifugation. Subsequently, chromatin was precipitated over night at 4°C with anti-H3K4me3 (NEB #9751 S) bound to Dynabeads® Protein A (Invitrogen #10002D). MinElute PCR Purification Kit (QIAGEN) was used to purify immunoprecipitated DNA after Proteinase K (Sigma-Aldrich) digestion at 65°C for 4h. 50ng of purified DNA was used for library preparation with the TruSeq ChIP sample preparation kit (Illumina) according to the manufacturer's instructions.