Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
Monocytes-CD14+
Tissue
monocytes
Lineage
mesoderm
Description
Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis

Attributes by original data submitter

Sample

ENA first public
2018-11-09
ENA last update
2018-04-23
ENA-CHECKLIST
ERC000011
External Id
SAMEA4603257
INSDC center alias
INSERM U1170
INSDC center name
INSERM U1170
INSDC first public
2018-11-09T17:03:22Z
INSDC last update
2018-04-23T17:23:55Z
INSDC status
public
Submitter Id
E-MTAB-6689:BC208/CTL2/H3K4Me3
broker name
ArrayExpress
cell type
CD14-positive, CD16-negative classical monocyte
common name
human
disease
normal
individual
BC208/CTL2
organism part
blood
sample name
E-MTAB-6689:BC208/CTL2/H3K4Me3

Sequenced DNA Library

library_name
BC208/CTL2/H3K4Me3_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) and from CMML patients, separated on Pancoll (Pan-Biotech, Dutscher, Brumath, France). Peripheral blood classical monocytes were sorted with magnetic beads and the AutoMacs system (Miltenyi Biotech, Paris), using the monocyte isolation kit II (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-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 cycles more.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
85379168
Reads aligned (%)
34.6
Duplicates removed (%)
51.2
Number of peaks
15201 (qval < 1E-05)

hg19

Number of total reads
85379168
Reads aligned (%)
33.2
Duplicates removed (%)
55.8
Number of peaks
14557 (qval < 1E-05)

Base call quality data from DBCLS SRA