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
peripheral blood
cell type
monocyte derived macrophages
initial differentiation
GM-CSF
activation stimuli
IL4, 72h
chip antibody
anti PU.1 (Santa Cruz Biotechnology, sc-352X, lot D2011)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixed or unfixed chromatin out of primary human macrophage lysates was sheared and histone-DNA or TF-DNA complexes isolated with antibody. Multiplex DNA libraries of both H3K4me3 as well as PU.1 bound DNA were generated using Illumina’s ChIP-Seq Sample Preparation Kit (Illumina; # IP-102-1001) and the Multiplexing Sample Preparation Oligonucleotide Kit (Illumina; # PE-400-1001) using approximately 10 ng DNA following the manufacturer’s instructions. Briefly, purified DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Klenow exo minus polymerase to generate a protruding 3′ A base used for adaptor ligation. Next, size selection of libraries was performed as follows: DNA libraries were agarose gel purified, DNA fragments with approximately 220 bp size excised and eluted using QIAquick Gel Extraction kit (Qiagen). After subsequent adapter ligation to the repaired ends, an amplification step was performed for 5 cycles with PCR primers 1.1 and 2.1 (Illumina; # IP-102-1001). During a second 13 cycles amplification step multiplex PCR primers were added to the DNA libraries to construct multiplex sequencing libraries. For PU.1 DNA libraries multiplex PCR primers were added directly after adapter ligation to the amplification mix and 18 cycles of amplification were performed. After amplification steps DNA was purified.

Sequencing Platform

instrument_model
Illumina HiScanSQ

hg19

Number of total reads
8050130
Reads aligned (%)
54.7
Duplicates removed (%)
7.5
Number of peaks
1269 (qval < 1E-05)

hg38

Number of total reads
8050130
Reads aligned (%)
56.1
Duplicates removed (%)
6.4
Number of peaks
1275 (qval < 1E-05)

Base call quality data from DBCLS SRA