Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
PBMC
Tissue
blood
Lineage
mesoderm
Description
peripheral blood mononuclear cells

Attributes by original data submitter

Sample

source_name
PBMC
individual
control
genotype
control
cell type
PBMC
chip antibody
H3K4me3 (Millipore, catalog# 07-473, lot# 2930138)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were sonicated using a Bioruptor UCD-200 sonicator (Diagenode). Sheared chromatin was immunoprecipitated with 2 μl of anti-H3K4me3 antibody (#07-473, Millipore) and 2 μl of Dynabeads M-280 magnetic beads (Sheep Anti-Mouse IgG, Sheep Anti-Rabbit IgG, Life Technologies) using the SX-8G IP-Star Automated System (Diagenode). ChIP samples were decrosslinked 65oC for 4 hr. After incubation the samples were treated with 0.2 mg/ml RNaseA (RNase Cocktail Enzyme Mix, Ambion, Life Technologies) and of 0.4 mg/ml ProteinaseK (Thermo Scientific). DNA was purified with DNA Clean kit & Concentrator TM-5 (Zymo Research) according to the manufacturer's protocol. Libraries were prepared using the supplied Ovation® Ultralow Systems Kit (NuGeneration Limited, England and Wales) according to the manufacturer's protocol. The barcoded libraries were quantified by Qubit 2.0 Fluorometer and validated with Agilent 2200 TapeStation analysis (Agilent Technologies, Inc.). Samples were sequenced with HiSeq 2500 (Illumina, San Diego, USA) producing 50 bp single-end sequences. Sequencing raw data was demultiplexed with CASAVA 1.8.2 software (Illumina, San Diego, USA).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
13964647
Reads aligned (%)
88.0
Duplicates removed (%)
15.3
Number of peaks
18306 (qval < 1E-05)

hg19

Number of total reads
13964647
Reads aligned (%)
87.5
Duplicates removed (%)
15.9
Number of peaks
18271 (qval < 1E-05)

Base call quality data from DBCLS SRA