Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

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

ENA first public
2015-06-01
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA3175642
INSDC center alias
Institute for molecular and tumor biology Philipps University Marburg Germany
INSDC center name
Institute for molecular and tumor biology Philipps University Marburg Germany
INSDC first public
2015-06-01T16:20:34Z
INSDC last update
2018-03-08T22:06:52Z
INSDC status
public
Submitter Id
E-MTAB-3166:TA004
broker name
ArrayExpress
cell type
tumor associated macrophage
common name
human
individual
OC46TAM
sample name
E-MTAB-3166:TA004

Sequenced DNA Library

library_name
TA004
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Ascites was collected from 30 patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committe After Ficoll gradient purification, cells were incubated in Greiner flasks in autologous ascites for 1 h at 37 degrees C in a humidified incubator with 5% CO2 (adherence selection). Nonadherent cells were removed by two PBS washing steps. Using a final concentration of 1% (w/v) formaldehyde for ten minutes at room temperature, proteins and DNA were crosslinked. After adding glycine to a final concentration of 125 mM, the cells were washed twice with ice-cold PBS. After harvesting by scraping and centrifugation, the pellet was resuspended in 1 ml hypotonic ChIP lysis buffer per 8x10^6 cells with protease inhibitors (Sigma) and incubated for 20 minutes. After centrifugation, nuclei were resuspended in ChIP lysis buffer II (RIPA) containing protease inhibitors and sheared with a Branson S250D using a microtip (52 pulses of 1 s, 2 s pause, 20% amplitude) with coolling (ice-ethanol). A 15 min 20,000xg supernatant was used for IP (after preclearing). ChIP was performed as in Adhikary and Mueller, Peroxisome Proliferator-Activated Receptors (PPARs) Methods in Molecular Biology Volume 952, 2013, pp 175-185. DNA was purified using Qiagen Minelute columns. Preceding the PE washing step, the membranes were washed twice with pure methanol in order to remove contaminating DNA-binding lipids that inhibit subsequent low-temperature enzymatic modification steps, which we found to be present in samples from primary macrophages. Libraries were synthesized from 1-2 ng of genomic DNA using the MicroPlex kit (Diagenode, Seraing, Belgium).

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
73491826
Reads aligned (%)
57.7
Duplicates removed (%)
46.7
Number of peaks
7021 (qval < 1E-05)

hg19

Number of total reads
73491826
Reads aligned (%)
57.2
Duplicates removed (%)
47.9
Number of peaks
6949 (qval < 1E-05)

Base call quality data from DBCLS SRA