Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4K20me3

Cell type

Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous

Attributes by original data submitter

Sample

source_name
human blood (chronic myelogenous leukemia)
cell type
K562 cell line - Somatic cells
chip antibody
H4K20me3 antibody (Diagenode Premium, C15410207)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001) to an average of 150-200 bp fragments as assessed by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). ChIP was performed manually with the iDeal ChIP-seq kit for Histones (Diagenode Cat# C01010059) Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP'd DNA (starting amount 1ng) using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Library amplification is assessed using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were then double size-selected and purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analyzed by High Sensitivity DNA Analysis Kit on a 2100 Bioanalyzer system (Agilent).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
33607052
Reads aligned (%)
97.5
Duplicates removed (%)
7.1
Number of peaks
1316 (qval < 1E-05)

hg19

Number of total reads
33607052
Reads aligned (%)
96.0
Duplicates removed (%)
9.1
Number of peaks
1302 (qval < 1E-05)

Base call quality data from DBCLS SRA