Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCFL

Cell type

Cell type Class
Bone
Cell type
TC-71
NA
NA

Attributes by original data submitter

Sample

source_name
TC-71 cells
antibody
BORIS
cell line
TC-71 cells
phase_of_therapy
post-chemotherapy
cell type
Ewing sarcoma cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with formaldehyde and lysed to obtain purified nuclei that were sonicated to shear chromatin. Protein-DNA complexes were then isolated using Dynabeads with corresponding antibodies, and DNA was isolated through reverse crosslinking and purified by phenol chloroform extraction in order to be used for library construction. Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit from NEB (E7645), according to the manufacturer's protocol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
29215924
Reads aligned (%)
94.7
Duplicates removed (%)
6.7
Number of peaks
1054 (qval < 1E-05)

hg38

Number of total reads
29215924
Reads aligned (%)
95.4
Duplicates removed (%)
5.3
Number of peaks
1150 (qval < 1E-05)

Base call quality data from DBCLS SRA