Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

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
human monoycte derived macrophages
pooled
yes
fully anonymized
yes
cell type
human monoycte derived macrophages
antibody
Sigma Imprint anti-GR, monoclonal

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
rinsed with PBS, fixed in 1% formaldehyde for 7.5min at RT, lysed and sonicated to fragment size 400-600bp. GR-DNA complexes were then isolated from soluble chromatin using Sigma Imprint anti GR monoclonal antibody , crosslinks reversed at 65 degrees and DNA cleaned up using Minielute columns(Qiagen) ChIP DNA samples were split into 3 aliquots and blunt ended with Klenow (Roche), PNK (NEB) and T4 DNA polymerase (Roche). An overhanging A base was added using Klenow (-exo) (NEB) and Illumina adapters ligated overnight at 16 degrees C with T4 DNA ligase (NEB). The IP samples were recombined after ligation and then split again into 7 aliquots. Libraries were amplified from each of these aliquots using Illumina Tru-seq multiplex primers and Phusion high-fidelity DNA polymerase (NEB) and the resulting material pooled and sequenced by Edinburgh Genomics on a Hiseq-2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
128537561
Reads aligned (%)
83.5
Duplicates removed (%)
49.1
Number of peaks
5513 (qval < 1E-05)

hg38

Number of total reads
128537561
Reads aligned (%)
84.8
Duplicates removed (%)
48.6
Number of peaks
5769 (qval < 1E-05)

Base call quality data from DBCLS SRA