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
Bone marrow derived macrophages
strain background
C57BL/6J
cell type
Bone marrow derived macrophages
genotype/variation
wild type
stimulated with
LPS for 3h
chip antibody
RelA (ab7970, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For the RelA and Ikaros ChIP, BMDMs were cross-linked with 1% formaldehyde for 10 min at room temperature. After cross-linking, chromatin was isolated from approximately 2 × 107 cells and 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 with a Bioruptor Plus (Diagenode) at medium setting for a total time of 17 min for Ikaros ChIP, 20 min for RelA ChIP, using a 30 sec ON, 30 sec OFF cycle to shear the chromatin to generate DNA fragments with a size range of 200 to 600 base pairs. The sonicated mixture was centrifuged at 14,000 rpm for 10 min. 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 the RelA ChIP, 10 ml of a rabbit polyclonal anti-RelA antibody (ab7970, Abcam) was diluted in 1 ml immune complex buffer with Dynabeads protein A (Invitrogen). For the Ikaros ChIP, 10 ul of a goat polyclonal Ikaros antibody ((M-20), Santa Cruz)) was diluted in 1 ml immune complex buffer with Dynabeads protein G (Invitrogen). 200 mg chromatin DNA was immunoprecipitated with antibody-bead complexes at 4oC overnight. The chromatin-DNA complexes were washed with immune complex buffers (Low salt, High salt, LiCl and TE) and were eluted followed by reverse cross-linking (10 mM Tris-HCl, 300 mM NaCl, 55 mM EDTA, 0.5% SDS). Sequencing libraries were generated using Illumina TruSeq V3 protocol and subjected to 51 bp single-end sequencing on an Illumina HiSeq2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
33960443
Reads aligned (%)
96.6
Duplicates removed (%)
23.8
Number of peaks
2290 (qval < 1E-05)

mm9

Number of total reads
33960443
Reads aligned (%)
96.4
Duplicates removed (%)
23.8
Number of peaks
2288 (qval < 1E-05)

Base call quality data from DBCLS SRA