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

Sample

source_name

K562

chip-antibody

None

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

16000000

Reads aligned (%)

32.1

Duplicates removed (%)

1.2

Number of peaks

57 (qval < 1E-05)

hg19

Number of total reads

16000000

Reads aligned (%)

31.4

Duplicates removed (%)

1.3

Number of peaks

31 (qval < 1E-05)