Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
Monocytes
MeSH Description
Large, phagocytic mononuclear leukocytes produced in the vertebrate BONE MARROW and released into the BLOOD; contain a large, oval or somewhat indented nucleus surrounded by voluminous cytoplasm and numerous organelles.

Attributes by original data submitter

Sample

ENA first public
2019-03-04
ENA last update
2017-12-18
ENA-CHECKLIST
ERC000011
External Id
SAMEA104441615
INSDC center alias
Inserm U1170
INSDC center name
Inserm U1170
INSDC first public
2019-03-04T17:03:23Z
INSDC last update
2017-12-18T17:12:36Z
INSDC status
public
Submitter Id
E-MTAB-6305:BC270 Mono CFMS
age
27
broker name
ArrayExpress
cell type
monocyte
common name
human
disease
normal
genotype
wild type
organism part
blood
phenotype
CD14 positive
sample name
E-MTAB-6305:BC270 Mono CFMS
sex
male

Sequenced DNA Library

library_name
BC270 Mono 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). 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 polyclonal anti-CSF-1R antibody (sc-692, 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

hg38

Number of total reads
61266401
Reads aligned (%)
91.3
Duplicates removed (%)
62.2
Number of peaks
3024 (qval < 1E-05)

hg19

Number of total reads
61266401
Reads aligned (%)
88.0
Duplicates removed (%)
65.6
Number of peaks
2331 (qval < 1E-05)

Base call quality data from DBCLS SRA