Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TOP2B

Cell type

Cell type Class
Blood
Cell type
KG-1
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
Topo-2B Antibody No Etoposide
cell line
KG-1
drug exposure
0 mins
drug
Methanol (vehicle)
antibody
Anti-Top2Beta (3535)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with fresh 1% formaldehyde for 10 min. and then washed with PBS and protease inhibitor cocktail. Chromatin precipitation was performed using EZ-Magna ChIP A kit (Merck-Millipore). Chromatin was fragmented with Bandelin Sano Plus HD70 sonicator in 6 15s cycles at 20% power. For each antibody three IPs with chromatin from about 2 * 10^6 cells each and 5 μg anti-Top2a antibody (3116) or 4 μg of anti-Top2b antibody (3535) were performed in 4°C for 4.5 h. Three INPUT samples for each treatment was prepared from 2.5 ul of chromatin (5%). After IP samples were treated with proteinase K for 2 h in 63°C and for additional 10 min in 90°C ChIP DNA was purified on spin columns and eluted with 30 μl of TE buffer. Samples of DNA immunoprecipitated with the same antibody were pooled together and stored in -80°C. Samples were used to construct Illumina paired-ends libraries at Source Bioscience using their protocol and sequenced on Illumina HiSeq2000 with 50 bp read-length.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
11431023
Reads aligned (%)
29.4
Duplicates removed (%)
82.5
Number of peaks
55 (qval < 1E-05)

hg38

Number of total reads
11431023
Reads aligned (%)
31.9
Duplicates removed (%)
81.3
Number of peaks
50 (qval < 1E-05)

Base call quality data from DBCLS SRA