Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Elf4

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); 7th day of differentiation
strain
C57BL/6
tissue
bone marrow
cell type
macrophage
days of differentiation
7
antibody
Elf4 home made antibody
treatment
No treatment

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Roughly 80 x 10^6 (for Fli1, Elf1 and Pol II ChIP-seq), 40 x 10^6 (for GABP-α, Elf4 ChIP-seq) or 5 x 10^6 (for PU.1 and histone modifications ChIP-seq) cells were fixed in 1% formaldehyde for 10min and were lysed with RIPA buffer, after chromatin shearing by sonication. Lysate was immunoprecipitated with 5-10 μg of antibody. Antibodies were pre-bound overnight to 50-100 μl of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM 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 libraries were prepared for HiSeq 2000 Illumina sequencing using a standard protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
26031534
Reads aligned (%)
95.2
Duplicates removed (%)
24.1
Number of peaks
18150 (qval < 1E-05)

mm9

Number of total reads
26031534
Reads aligned (%)
94.9
Duplicates removed (%)
24.1
Number of peaks
18166 (qval < 1E-05)

Base call quality data from DBCLS SRA