Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

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

source_name
Primary Monocytes(BC12)
cell type
Primary Monocytes(BC12)

Sequenced DNA Library

library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using HiSeq 2000 as recommended by the manufacturer. DNaseI treatment was done on isolated nuclei for 3 minutes and reaction was stopped with stop buffer ( 50mM Tris-HCl, pH 8, 100mM NaCl, 0.10% SDS, 100mM EDTA, pH 8.0, 1mM Spermidine, 0.3mM Spermine), sample was further fractionated on 9% Sucrose gradient for 24hrs/25000rpm at 16ºC . Further sequenced using HiSeq as recommended by the manufacturer.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
29329308
Reads aligned (%)
95.4
Duplicates removed (%)
3.4
Number of peaks
11076 (qval < 1E-05)

hg19

Number of total reads
29329308
Reads aligned (%)
94.3
Duplicates removed (%)
4.1
Number of peaks
10510 (qval < 1E-05)

Base call quality data from DBCLS SRA