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 osteosarcoma cell line
cell line
U2OS
cell cycle phase
Interphase
replicate
2
antibody
CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min and neutralized with 0.125 M glycine for 5 min . After sonication, 25 ug of chromatin was incubated with 5 μg of anti-H3K4me3, anti-H3K4me1, anti-H3K27ac, or anti-CTCF antibodies at 4°C overnight. For spike-in normalization, 50 ng of Spike-in chromatin (53083, Active Motif) with 2 μg Spike-in antibody were added. Immunoprecipitated complexes were collected using Dynabeads M280 sheep-anti-rabbit IgG (Invitrogen). Subsequently, immuno-complexes were washed, decorsslinked and DNA was purified by QIAquick Spin columns (Qiagen). Cells (5 × 106) were cross-linked with 1% formaldehyde for 10 min, and ChIP-seq was performed as previously described (Toyama et al. 2018). Spike-in was carried out according to vendor protocols (Active Motif). Briefly, DNA libraries were generated using the Kapa Hyper Prep Kit for Illumina Platforms (Kapa biosystems). Libraries were sequenced in a NextSeq 500 system (Illumina). ChIP-seq libraries were generated using the Kapa Hyper Prep Kit for Illumina Platforms (Kapa biosystems).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
4017699
Reads aligned (%)
80.7
Duplicates removed (%)
14.2
Number of peaks
431 (qval < 1E-05)

hg38

Number of total reads
4017699
Reads aligned (%)
82.6
Duplicates removed (%)
9.6
Number of peaks
471 (qval < 1E-05)

Base call quality data from DBCLS SRA