Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ATF2

Cell type

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.)

Attributes by original data submitter

Sample

source_name
Peripheral blood monocyte-derived macrophages
treatment
IL10
replicate
Not applicable
chip target
ATF2 (C-terminus)
library type
ATF2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10 million macrophages per sample were cultured in 10 cm culture dishes, treated with or without IL-10 (10 ng/mL) for 24 hours. Following treatment incubation, Plates were rinsed once with room temperature PBS, and fixed using 1% formaldehyde for 10 minutes on an orbital shaking platform set to slowly mix the fluid. The fixation reaction was then quenched by adding glycine to a final concentration of 0.15 M and incubating a further 5 minutes. Plates were then rinsed 1x with ice-cold PBS containing protease inhibitors and harvest from the plate by scraping. Cells were centrifuged in 15 mL conical tubes 5 minutes at 300 x G at 4°C. Immunoprecipitation was carried out as following the method of Blecher-Gonen (Blecher-Gonen et al., Nat Protoc. 2013 Mar;8(3):539-54.), with the following modifications: sonication was performed using a Covaris S2 instrument in 1 mL tubes, 20 million cells per tube, intensity 5, duty cycle 20%, 200 cycles per burst for 6 minutes; 75 μl Protein G microbeads (Invitrogen) and 3 ug of H3K27ac antibody (Abcam ab 4729) were used. Illumina sequencing libraries were prepared using the NEBNext ChIPseq library prep kit (NEB).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
119626901
Reads aligned (%)
59.7
Duplicates removed (%)
32.6
Number of peaks
5963 (qval < 1E-05)

hg38

Number of total reads
119626901
Reads aligned (%)
61.8
Duplicates removed (%)
31.0
Number of peaks
6351 (qval < 1E-05)

Base call quality data from DBCLS SRA