Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
K562
cell line
K562
treatment
Untreated
antibody
Input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Sequencing libraries were constructed from DNA samples with the Illumina TruSeq V3 library construction protocol. Cells were treated as indicated, crosslinked with 1% formaldehyde in PBS for 10 min, followed by quenching with 125 mM glycine. Cells were then resuspended in lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% nonidet P-40) to isolate nuclei. Nuclei were resuspended in micrococcal nuclease (MNase) digestion buffer (10 mM Tris pH 7.4, 15 mM NaCl, 60 mM KCl, 0.15 mM spermine, 0.5 mM spermidine) and 1.2 U/µl MNase was added for 30-45 min at 37 °C. The reaction was stopped by adding 50 mM EDTA and nuclear pellets were resuspended in 10mM Tris-HCl (pH8.0), 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine. Lysates were sonicated briefly to disrupt nuclear membranes using an ultra sonicator water bath (Bioruptor, Diagenode). Diluted lysates were incubated o/n at 4 °C with the indicated antibodies after addition of 1% Triton X-100. IPs were performed using 30 µl Protein A/G magnetic beads (Pierce). Eluted DNA was purified with QIAquick PCR purification (Qiagen) according to the manufacturer instructions. Purified ChIP DNA was analyzed by qPCR using a LightCycler 480 II (Roche). Sequencing libraries were constructed from DNA samples (ChIP and control samples) with the Illumina TruSeq V3 library construction protocol (Illumina, San Diego, USA).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
172122598
Reads aligned (%)
97.6
Duplicates removed (%)
11.1
Number of peaks
1713 (qval < 1E-05)

hg19

Number of total reads
172122598
Reads aligned (%)
96.6
Duplicates removed (%)
13.1
Number of peaks
1325 (qval < 1E-05)

Base call quality data from DBCLS SRA