Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

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
chip-antibody
H3K27me3 - Cell Signaling (9751B)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were rinsed with PBS and treated at 37C with MNase for 5 min, before quenching with MNase stop buffer and the chromatin was sheared to 200-500 bp fragments using a Fisher Dismembrator. Chromatin fragments were immunoprecipitated with specific antibodies at 4 °C with gentle rotation. Antibody-chromatin complexes were washed and eluted and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing. 20-50 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
11642155
Reads aligned (%)
24.8
Duplicates removed (%)
0.8
Number of peaks
29 (qval < 1E-05)

hg19

Number of total reads
11642155
Reads aligned (%)
24.3
Duplicates removed (%)
1.0
Number of peaks
17 (qval < 1E-05)

Base call quality data from DBCLS SRA