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
2018-11-09
ENA last update
2018-10-16
ENA-CHECKLIST
ERC000011
External Id
SAMEA4975960
INSDC center alias
INSERM U1170
INSDC center name
INSERM U1170
INSDC first public
2018-11-09T17:03:27Z
INSDC last update
2018-10-16T13:25:01Z
INSDC status
public
Submitter Id
E-MTAB-7290:CTL5-Classical-input
age
18 to 65
broker name
ArrayExpress
cell type
classical monocyte
common name
human
developmental stage
adult
disease
normal
individual
2
organism part
blood
sample name
E-MTAB-7290:CTL5-Classical-input
sex
female

Sequenced DNA Library

library_name
CTL5-Classical-input_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Monocytes subsets were first enriched from mononuclear cells by negative selection using CD19-, CD56-, CD3-, CD16-microbeads and the AutoMacs system (Miltenyi Biotech), then sorted using CD45, CD14, and CD16 antibodies after exclusion of CD56+ cells and a cell sorter. Cells were cross-linked with addition of 1% formaldehyde to the culture medium for 10 min at room temperature with agitation. Fixation was stopped by addition of 125mM glycine during 5 min at RT with agitation before washing samples twice in ice-cold PBS and adding SDS lysis buffer (Millipore, 10uL per 1.10^6 cells) supplemented with 1% protease inhibitor cocktail (Active Motif). Samples were incubated 15 min on ice before storage at -80°C. Cross-linked DNA were sonicated using 12x24 mm round bottom tube, 10 min at 40W (Covaris S220, Woodingdean, UK). Chromatin immunoprecipitation was carried out using ChIP-it express kit according to manufacturer's instruction (Active Motif) with a polyclonal anti-H3K4me3 antibody (39159, Active Motif). 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 more cycles.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
20714639
Reads aligned (%)
57.9
Duplicates removed (%)
7.7
Number of peaks
49 (qval < 1E-05)

hg19

Number of total reads
20714639
Reads aligned (%)
57.0
Duplicates removed (%)
7.8
Number of peaks
35 (qval < 1E-05)

Base call quality data from DBCLS SRA