Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
Mock-treated K562 erythroleukemia cells
experiment
CTCF ChIP-seq
treatment
K562 cells were treated with 5-aza-2’-deoxycytidine (decitabine; Sigma, A3656) dissolved in DMSO to 10mM. Drug was administered at 1uM daily for 3 days. Control K562 cells were mock treated with DMSO.
replicate
2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 degrees C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing. 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
37001145
Reads aligned (%)
25.0
Duplicates removed (%)
1.2
Number of peaks
11757 (qval < 1E-05)

hg19

Number of total reads
37001145
Reads aligned (%)
24.6
Duplicates removed (%)
1.9
Number of peaks
11633 (qval < 1E-05)

Base call quality data from DBCLS SRA