Sample information curated by ChIP-Atlas

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.)

Attributes by original data submitter

Sample

source_name
Macrophages(BC8)
cell type
Macrophages(BC8)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using HiSeq 2000 as recommended by the manufacturer. DNaseI treatment was done on isolated nuclei for 3 minutes and reaction was stopped with stop buffer ( 50mM Tris-HCl, pH 8, 100mM NaCl, 0.10% SDS, 100mM EDTA, pH 8.0, 1mM Spermidine, 0.3mM Spermine), sample was further fractionated on 9% Sucrose gradient for 24hrs/25000rpm at 16ºC . Further sequenced using HiSeq as recommended by the manufacturer.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
18593913
Reads aligned (%)
97.7
Duplicates removed (%)
35.2
Number of peaks
3737 (qval < 1E-05)

hg19

Number of total reads
18593913
Reads aligned (%)
97.0
Duplicates removed (%)
36.0
Number of peaks
3767 (qval < 1E-05)

Base call quality data from DBCLS SRA