Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CSF1R

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

Alias
E-MTAB-6305:Donor1/BC212 Macrophage CFMS
Broker name
ArrayExpress
Description
Protocols: Peripheral blood mononucleated cells (PBMC) were obtained from healthy donor buffy coats (Etablissement Français du sang, Rungis, France) or CMML whole blood, separated on Pancoll (Pan-Biotech, Dutscher, Brumath, France). Peripheral blood CD14+ monocytes were sorted with magnetic beads and the AutoMacs system (Miltenyi Biotech, Paris, France). After sorting, monocytes were cultured overnight at 1 million cells/mL in RPMI 1640 Glutamax medium (ThermoFisher Scientific) supplemented with 10% heat inactivated fetal bovine serum (FBS, Lonza, Amboise, France), 1% penicillin/streptomycin and 2mM L-Glutamine (ThermoFisher Scientific). Monocytes were seeded at 0.5 million cells/mL and differentiated into macrophages in the same medium containing recombinant human CSF-1 (100ng/mL Peprotech, Neuilly-Sur-Seine, France) during 6h to 3 days. Cells were cross-linked with addition of 1% formaldehyde directly to the culture medium for 10 min at RT with agitation. Fixation was stopped by addition of 125mM glycin during 5 min at RT with agitation and samples were then washed 2 times in ice-cold PBS before addition of SDS lysis buffer (Millipore, 10uL per 1.106 cells) supplemented with 1% protease inhibitor cocktail (Active Motif). Samples were vortexed and incubated 15 min on ice before 10 min sonication at 40W (Covaris S220, Woodingdean, UK). The chromatin immunoprecipitation was carried out using ChIP-it express kit according to manufacturer's instruction (Active Motif) with a monoclonal anti-CSF-1R antibody (sc-46662, santa cruz bioechnology). Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an 'A' base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bioo Scientific, Proteigene, Saint Marcel, France) using the Bravo Platform (Agilent, Les Ulis, France), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter, Villepinte, France) and amplified by PCR for 10 cycles more.
ENA checklist
ERC000011
INSDC center alias
Inserm U1170
INSDC center name
Inserm U1170
INSDC first public
2019-03-04T17:03:23Z
INSDC last update
2017-12-18T17:12:35Z
INSDC status
public
SRA accession
ERS2059540
Sample Name
ERS2059540
Title
Donor1/BC212 Macrophage CFMS
age
59
cell_type
macrophage
disease
normal
genotype
wild type
growth condition
72h RPMI 10 percent FBS
organism
Homo sapiens
organism part
blood
phenotype
wild type phenotype
sex
male
stimulus
CSF-1; 100 nanogram per milliliter

Sequenced DNA Library

library_name
Donor1/BC212 Macrophage CFMS_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Peripheral blood mononucleated cells (PBMC) were obtained from healthy donor buffy coats (Etablissement Français du sang, Rungis, France) or CMML whole blood, separated on Pancoll (Pan-Biotech, Dutscher, Brumath, France). Peripheral blood CD14+ monocytes were sorted with magnetic beads and the AutoMacs system (Miltenyi Biotech, Paris, France). After sorting, monocytes were cultured overnight at 1 million cells/mL in RPMI 1640 Glutamax medium (ThermoFisher Scientific) supplemented with 10% heat inactivated fetal bovine serum (FBS, Lonza, Amboise, France), 1% penicillin/streptomycin and 2mM L-Glutamine (ThermoFisher Scientific). Monocytes were seeded at 0.5 million cells/mL and differentiated into macrophages in the same medium containing recombinant human CSF-1 (100ng/mL Peprotech, Neuilly-Sur-Seine, France) during 6h to 3 days. Cells were cross-linked with addition of 1% formaldehyde directly to the culture medium for 10 min at RT with agitation. Fixation was stopped by addition of 125mM glycin during 5 min at RT with agitation and samples were then washed 2 times in ice-cold PBS before addition of SDS lysis buffer (Millipore, 10uL per 1.106 cells) supplemented with 1% protease inhibitor cocktail (Active Motif). Samples were vortexed and incubated 15 min on ice before 10 min sonication at 40W (Covaris S220, Woodingdean, UK). The chromatin immunoprecipitation was carried out using ChIP-it express kit according to manufacturer's instruction (Active Motif) with a monoclonal anti-CSF-1R antibody (sc-46662, santa cruz bioechnology). Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an 'A' base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bioo Scientific, Proteigene, Saint Marcel, France) using the Bravo Platform (Agilent, Les Ulis, France), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter, Villepinte, France) and amplified by PCR for 10 cycles more.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
77131861
Reads aligned (%)
16.6
Duplicates removed (%)
65.2
Number of peaks
1514 (qval < 1E-05)

hg38

Number of total reads
77131861
Reads aligned (%)
17.9
Duplicates removed (%)
63.1
Number of peaks
1846 (qval < 1E-05)

Base call quality data from DBCLS SRA