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

treatment

BCG iv

mouse id

BCGiv_BMDM_10

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems). ATAC-seq libraries were generated from 100,000 BMDMs, as previously described (Buenrostro et al., 2013) and sequenced on an Illumina HiSeq 2500 using 100-bp paired-end reads. We performed ATAC-seq on non-infected BMDMs from four PBS-control mice and three BCG-iv vaccinated mice.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

49498725

Reads aligned (%)

80.1

Duplicates removed (%)

20.0

Number of peaks

21201 (qval < 1E-05)

mm9

Number of total reads

49498725

Reads aligned (%)

80.0

Duplicates removed (%)

20.0

Number of peaks

21169 (qval < 1E-05)