Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

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

Bone marrow-derived macrophages

cell type

Bone marrow-derived macrophages

stimulation

1 hour of LPS stimulation

genotype

Rad21-/-

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Nuclei suspensions were prepared from 50,000 cells per biological replicate. ATAC sequencing was performed as described in (Buenrostro, J.D., P.G. Giresi, L.C. Zaba, H.Y. Chang, and W.J. Greenleaf. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods. 10:1213–1218. )

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

52973949

Reads aligned (%)

60.1

Duplicates removed (%)

19.8

Number of peaks

6968 (qval < 1E-05)

mm9

Number of total reads

52973949

Reads aligned (%)

60.0

Duplicates removed (%)

19.8

Number of peaks

6946 (qval < 1E-05)