Antigen

Antigen Class

Unclassified

Antigen

Unclassified

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.)

Sample

source_name

Macrophage-control

treatment

Control buffer

gender

male

cell type

Macrophage

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

FAIRE enriched genomic DNA was extracted using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67). Libraries were generated from gel-purified ~200bp DNA fragments (actual fragment size median 151bp +-39 median absolute deviation (MAD) for samples numbered 279, 280, 277, 278 and 141+-32 MAD for samples 205, 207). After adapter ligation and PCR-based amplification, samples were sequenced on the Illumina HiSeq platform to generated paired end 50bp reads (Illumina, San Diego, CA). Samples were multiplexed across 2 lanes.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

47440938

Reads aligned (%)

97.0

Duplicates removed (%)

4.8

Number of peaks

10206 (qval < 1E-05)

hg19

Number of total reads

47440938

Reads aligned (%)

95.4

Duplicates removed (%)

5.7

Number of peaks

9231 (qval < 1E-05)