Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
Bone marrow-derived macrophages
cell type
Bone marrow-derived macrophages
stimulation
6 hours of LPS stimulation
genotype
wild-type
chip antibody
-

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RAD21 ChIP cells were crosslinked (1% formaldehyde), lysed and sonicated a Bioruptor for 25 cycles at power H in RAD21 sonication buffer (1% Triton, 0.1% Sodium Deoxycholate, 0.1% SDS, 0.8M NaCl, 10mM Tris, 1mM EDTA). Then they were imunoprecipitated over-night using a-Rad21 (ab992, Abcam), incubated with Dynabeads Protein G, washed, decrosslinked and purified. Libraries were prepared using a NEBNext Ultra DNA LIbrary Prep kit (New England Biolabs E7370) and assessed for quality and quantity with Bioanalyzer and Qubit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
37297789
Reads aligned (%)
98.8
Duplicates removed (%)
13.9
Number of peaks
619 (qval < 1E-05)

mm9

Number of total reads
37297789
Reads aligned (%)
98.5
Duplicates removed (%)
13.9
Number of peaks
680 (qval < 1E-05)

Base call quality data from DBCLS SRA