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
human K562 cell_Etoposide_amp
biomaterial_provider
ATCC CCL 243
cell line
K562
replicate
1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Ten million vehicle or TOP2 poison-treated K562 cells were lysed with RIPA buffer and the lysates sonicated to fragment the DNA to 250-750bp. TOP2A was immunocaptured with anti-TOP2A IgG and Protein G magnetic beads, the bead-bound fraction separated, and immunoprecipitation repeated twice on non-bound fractions. The bead-bound fractions were combined and treated with CIP (NEB) to detach the TOP2A-bound DNA from cleavage complexes. The released DNA and input DNA from sonicated lysates were purified and used directly for library synthesis with an IlluminaTruSeq ChIP library kitor pre-amplified with a SEQXE kit (Sigma) before library preparation. Sequencing was performed on an Illumina HiSeq2500 (SE50 protocol)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
45553707
Reads aligned (%)
95.5
Duplicates removed (%)
64.3
Number of peaks
2086 (qval < 1E-05)

hg19

Number of total reads
45553707
Reads aligned (%)
94.5
Duplicates removed (%)
66.3
Number of peaks
1943 (qval < 1E-05)

Base call quality data from DBCLS SRA