Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TOP2B

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7 Cells
cell line
MCF7
agent
untreated control
time
0 mins
antibody
Anti-Top2Beta (3535+30400) [made in-house]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with formaldehyde (1% (v/v), Sigma-Aldrich Inc.), neutralised with glycine, washed with 1XPBS and trypsinised (0.05% trypsin in 0.53mM EDTA (Invitrogen Inc. 25300-054). Cells were collected and lysed with cell lysis buffer +PI, collected and resuspended in nuclear lysis buffer +PI. Chromatin was sonicated to between 500-1000bp, 14x15sec cycles, and 5% was removed as “input”. 10.6μg of polyclonal anti-TOP2B antisera was added to protein A magnetic beads (Invitrogen, 100.02D). Chromatin was diluted, incubated with the beads and rotated at 4°C for 4.5hrs. IP’s were washed, Low Salt Buffer, High Salt Buffer, LiCl Buffer and TE Buffer respectively, resuspended in ChIP Elution Buffer+Proteinase K, rotated at 65°C for 2 hours followed by incubation at 95°C for 10 minutes. DNA was then purified using spin columns. 6-21ng/μl of DNA was sent for Illumina ChIP Sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
55322578
Reads aligned (%)
18.5
Duplicates removed (%)
77.6
Number of peaks
1035 (qval < 1E-05)

hg38

Number of total reads
55322578
Reads aligned (%)
20.4
Duplicates removed (%)
75.5
Number of peaks
449 (qval < 1E-05)

Base call quality data from DBCLS SRA