Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rela

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
Dex 3h pre, 0h LPS RelA
strain
C57BL/6J
cell type
Bone marrow derived macrophages
treatment
Dex 3h pre, 0h LPS RelA
chip antibody
RelA (Ab7970, Abcam) and Dynabeads Protein A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RelA ChIP, BMDMs were subject to crosslinking with 1% formaldehyde for 10 minutes at room temperature. For GR ChIP, we used a dual crosslinking method (Uhlenhaut et al., 2013) to detect both tethered and directly bound chromatin. BMDMs were subject to crosslinking with 2mM disuccinimidyl glutarate (DSG) for 30 min followed by 1% formaldehyde for 10 min at room temperature. After crosslinking, chromatin was isolated from about 4 × 10^7 cells, which allows 2 to 3 different immunoprecipitations per sample at a time, and then processed as follows. The lysis buffer to shear the chromatin contained 0.5% SDS, 10 mM EDTA (pH 8), 50 mM tris-HCl (pH 8), and proteinase inhibitor cocktail. Sonication was performed to shear the chromatin to generate DNA fragments with a size range of 400 to 500 base pairs. The sheared chromatin samples were diluted 1:5 in dilution buffer (0.01% SDS, 1.1% Triton-X, 1.2 mM EDTA (pH 8), 20 mM tris-HCl (pH 8), 167 mM NaCl, and proteinase inhibitor cocktail). For each ChIP, 200 µg chromatin DNA was precipitated with antibody coated bead complexes (Dynabeads Protein A for RelA ChIP; anti-IgG paramagnetic beads for GR ChIP, Invitrogen). 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
26272702
Reads aligned (%)
96.9
Duplicates removed (%)
17.5
Number of peaks
400 (qval < 1E-05)

mm9

Number of total reads
26272702
Reads aligned (%)
96.7
Duplicates removed (%)
17.5
Number of peaks
442 (qval < 1E-05)

Base call quality data from DBCLS SRA