Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Stat2

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
STAT2 (santa crus, sc-950)
treatment
No treatment

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 5-10ug of antibody. Antibodies were pre-bound overnight to 50-100ul 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 was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
18737183
Reads aligned (%)
91.7
Duplicates removed (%)
23.5
Number of peaks
560 (qval < 1E-05)

mm9

Number of total reads
18737183
Reads aligned (%)
91.5
Duplicates removed (%)
23.6
Number of peaks
583 (qval < 1E-05)

Base call quality data from DBCLS SRA