Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Atf3

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
C57BL/6
genotype
wildtype
stimulus
lipid A
time
30 min
chip antibody
ATF3 (Santa Cruz, catalog# sc-188, lot# L2214)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Forty million of bone marrow-derived macrophages were cross-linked with 4mM DSG for 1 hr and 1% formaldehyde for 10 min. Nuclei pellets were isolated and sonicated using Misonix 3000 sonicator to fragments between 200bp to 1000bp. Chromatin lysate was incubated with the antibody overnight. The immune complexes were pulled down with Protein G Dynabeads (Invitrogen, 10004D) and washed for four times. The purified immune complexes were incubated with proteinase K at 60°C overnight for reverse cross-linking and protein digestion. IP DNA was purified by phenol-chloroform. DNA concentration was quantified by Qubit kit (Thermo Fisher, Q32854). ChIP-seq library was prepared using KAPA LTP library preparation kit (KK8500) following the manufacturer’s instructions. About 10ng DNA was used following the standard end repair, A-tailing, and adapter ligation steps. Each library was amplified with fewer than 12 PCR cycles. An additional size selection was performed after PCR to remove the big fragments. The final library size is between 300bp to 600bp.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
31120409
Reads aligned (%)
95.5
Duplicates removed (%)
13.9
Number of peaks
20952 (qval < 1E-05)

mm9

Number of total reads
31120409
Reads aligned (%)
95.2
Duplicates removed (%)
13.9
Number of peaks
20955 (qval < 1E-05)

Base call quality data from DBCLS SRA