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
Cells were crosslinked with 1% formaldehyde, lysed and then sonicated using a Bioruptor instrument (Diagenode) for 40 cycles and power H in sonication buffer (1% Triton, 0.1% Sodium Deoxycholate, 0.5% SDS, 0.2M NaCl, 10mM Tris, 10mM EDTA). Lysates were immunoprecipitated overnight with a-H3 (Abcam ab1791) and a-H3K27Ac (Abcam ab4729) pre-bound to Dynabeads Protein G (Invitrogen 10004D) in RIPA buffer. Beads were washed and reverse-crosslinked by incubation at 65ºC in 10% SDS. DNA was purified using ChIP DNA clean & Concentrator Kit (Zymo D5205). 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
28525927
Reads aligned (%)
98.4
Duplicates removed (%)
14.9
Number of peaks
440 (qval < 1E-05)

mm9

Number of total reads
28525927
Reads aligned (%)
98.2
Duplicates removed (%)
14.9
Number of peaks
479 (qval < 1E-05)

Base call quality data from DBCLS SRA