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 Input Control Treated ChIP-seq
cell line
K562
cell type
myelogenous leukemia cell line
treated with
0.5 mM NaBut
duration of treatment
72 hours

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin sonicated with Bioruptor (Diagenode) for 45 min.( 30 sec. on/off, High) in 1x RIPA buffer and aliquot was reserved for input control. Crosslinking was reversed with overnight 65°C incubation in 1% SDS, 0.1M sodium bicarbonate buffer and DNA was eluted with a PCR cleanup kit (Qiagen). Following TruSeq adapter ligations, DNA fragments were separated from free adapters by AmpureXL bead size selection steps and PCR amplification was performed for 18 cycles. ~20 million cells crosslinked with 1% formaldehyde for 10 min. at RT, quenched with glycine, and lysed with 1x RIPA buffer.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
21721702
Reads aligned (%)
96.5
Duplicates removed (%)
2.3
Number of peaks
935 (qval < 1E-05)

hg19

Number of total reads
21721702
Reads aligned (%)
95.6
Duplicates removed (%)
3.5
Number of peaks
923 (qval < 1E-05)

Base call quality data from DBCLS SRA