Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Bone
Cell type
U2OS
Tissue
bone
Lineage
mesoderm
Description
osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590)

Attributes by original data submitter

Sample

source_name
U2OS
cell line
U2OS
RNAi
none
damid tagged factor
none
antibody source
CTCF (ActiveMotif: #61311, lot# 16712001)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: cells were cross-linked with 1% formaldehyde at room temperature for 10 min and neutralized with 0.125 M glycine. After sonication,chromatin was incubated with 5–10 μg of antibody at 4°C overnight. Immunoprecipitated complexes were collected using Dynabeads M280 sheep-anti-rabbit IgG or sheep-anti-mouse IgG (Invitrogen). Subsequently, immuno-complexes were washed, decorsslinked and DNA was purified by QIAquick Spin columns (Qiagen). ChIP-Seq and DamID-Seq libraries were generated using the TruSeq ChIP sample Prep kit (Illumina) or the Kapa Hyper Prep Kit for Illumina Platforms followed by Illumina sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
37062425
Reads aligned (%)
76.3
Duplicates removed (%)
5.8
Number of peaks
19627 (qval < 1E-05)

hg38

Number of total reads
37062425
Reads aligned (%)
77.2
Duplicates removed (%)
4.3
Number of peaks
19848 (qval < 1E-05)

Base call quality data from DBCLS SRA