Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TOP2B

Cell type

Cell type Class
Neural
Cell type
Glioma
MeSH Description
Benign and malignant central nervous system neoplasms derived from glial cells (i.e., astrocytes, oligodendrocytes, and ependymocytes). Astrocytes may give rise to astrocytomas (ASTROCYTOMA) or glioblastoma multiforme (see GLIOBLASTOMA). Oligodendrocytes give rise to oligodendrogliomas (OLIGODENDROGLIOMA) and ependymocytes may undergo transformation to become EPENDYMOMA; CHOROID PLEXUS NEOPLASMS; or colloid cysts of the third ventricle. (From Escourolle et al., Manual of Basic Neuropathology, 2nd ed, p21)

Attributes by original data submitter

Sample

source_name
TS543 glioma cells
agent
ETO
genotype
TS543
cell type
glioma cells
chip antibody
TOP2B

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
18421760
Reads aligned (%)
56.5
Duplicates removed (%)
43.4
Number of peaks
5050 (qval < 1E-05)

hg38

Number of total reads
18421760
Reads aligned (%)
56.7
Duplicates removed (%)
43.2
Number of peaks
5051 (qval < 1E-05)

Base call quality data from DBCLS SRA