Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Hdac3

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
wild type
cell type
unstimulated bone marrow derived macrophages
chip antibody
HDAC3 (sc-11417) (Santa Cruz Biotechnology)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq analysis, formalin-fixed cells were sonicated and processed for immunoprecipitation. Briefly, 1.5 X 10^7 BMMs were crosslinked for 10 min. in 1% paraformaldehyde, washed and lysed. Chromatin was sheared by sonication (5 x 60 s at 30% maximum potency) to fragments of approximately 150bp. The sheared chromatin was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with antibodies against either HDAC3 or NCOR2, washed and eluted. The eluted chromatin was reverse-cross-linked, and DNA was purified using phenol/chloroform/isoamyl extraction. The purified ChIP DNA was prepared for sequencing with the Illumina ChIPSeq Sample Prep kit and processed in according to the manufacturer’s protocol. Sequencing was performed by Covance, Seattle, WA. Libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
20717974
Reads aligned (%)
90.8
Duplicates removed (%)
81.4
Number of peaks
255 (qval < 1E-05)

mm9

Number of total reads
20717974
Reads aligned (%)
90.5
Duplicates removed (%)
81.6
Number of peaks
260 (qval < 1E-05)

Base call quality data from DBCLS SRA