Antigen

Antigen Class

DNase-seq

Antigen

DNase-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

Dex late-treated 8h LPS

strain

C57BL/6J

cell type

Bone marrow derived macrophages

treatment

Dex late-treated 8h LPS

Sequenced DNA Library

library_strategy

DNase-Hypersensitivity

library_source

GENOMIC

library_selection

DNase

library_construction_protocol

After treatment with Dex and/or LPS, nuclei of BMDMs were isolated, and chromatin were digested with 80 U/ml DNase I (Sigma) for 3 min at 37 ºC and incubated at 55 ºC overnight with 10 µg/ml of RNaseA (Invitrogen) and Proteinase K (Ambion). Digested DNA fragments were purified using phenol-chloroform and enriched by size selection over sucrose gradient. DNA fragments between 100 bp and 500 bp were precipitated and dissolved in nuclease free H2O. Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

29480060

Reads aligned (%)

97.0

Duplicates removed (%)

15.4

Number of peaks

28362 (qval < 1E-05)

mm9

Number of total reads

29480060

Reads aligned (%)

96.7

Duplicates removed (%)

15.4

Number of peaks

28357 (qval < 1E-05)