Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Spi1

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
Primary bone marrow-derived macrophages (BMDM)
strain
C57BL/6
cell type
BMDM cells (7th day of differentiation)
antibody
Anti-PU.1 (in-house rabbit polyclonal against the N-Terminal (aa. 1-100))
retroviral infection
empty (sh-Renilla)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP lysates were generated from 5x10^8 cells. Cells were fixed in 1% formaldehyde for 10 min. Lysate was sonicated and then immunoprecipitated with 5 ug of antibody against PU.1 (or normal rabbit IgG as control). Antibodies were pre-bound overnight to 50 ul of G protein-coupled paramagnetic beads (Dynabeads) in PBS/0.5% BSA and then incubated with the lysates overnight at 4 C. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50 mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq2000 sequencing following standard protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
28567181
Reads aligned (%)
21.5
Duplicates removed (%)
28.0
Number of peaks
18100 (qval < 1E-05)

mm9

Number of total reads
28567181
Reads aligned (%)
21.4
Duplicates removed (%)
28.4
Number of peaks
18142 (qval < 1E-05)

Base call quality data from DBCLS SRA