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 human macrophages
cell type
peripheral blood derived macrophage
treatment
GM-CSF (72h)
chip antibody
PU.1 polyclonal rabbit antibody (SantaCruz, sc-352)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from 0.5x10E6 macrophages was cross-linked for ChIP reactions with 1 % formaldehyde. Nuclei were lysed and chromatin was sheared with the Covaris S220 ultrasound system. For ChIP antibody reactions a PU.1 polyclonal rabbit antibody was used (SantaCruz, sc-352). Washing and DNA purifications as well as size selections were performed with AMPure XP SPRI beads (Beckman Coulter). Published library construction protocol was adapted (Blecher-Gonen et al., Nature Protocols, 2013) and performed with 0.5 ng ChIP DNA. Barcodes from the NEXTflex adapter oligonucleotides kit (Bioo Scientific) were ligated to the ChIP-seq DNA fragments. Final DNA purification with additional size selection was performed with SPRI beads. ChIP-seq libraries were sequenced on the HiScanSQ/Hiseq 1000 sequencer (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg19

Number of total reads
35534732
Reads aligned (%)
75.5
Duplicates removed (%)
23.3
Number of peaks
101843 (qval < 1E-05)

hg38

Number of total reads
35534732
Reads aligned (%)
76.3
Duplicates removed (%)
22.9
Number of peaks
102031 (qval < 1E-05)

Base call quality data from DBCLS SRA