Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
cell type
Osteosarcoma cell line
chip antibody
none
treatment
control

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Native chromatin, digested with MNase was pre-cleared, SDS was added to 0.1% and incubated on ice for 12 min. IP buffer with inhibitors was added to 1x concentration (20 mM Tris pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100). After storing 10% of the material for Input sample, aliquots were made and H3S57 antibody (8 μg) (each ChIP with approximately 10M cells) and incubated for 14 h with rotation at 4°C. Pre-washed 20 μl beads slurry per sample (Dynabeads protein A) pre-blocked in 5 mg/ml BSA in PBS were incubated and incubated for 2 h. The beads were washed with a total of 3 ml of each: wash A (50 mM Tris, 10 mM EDTA, 75 mM NaCl), wash B (wash A but with 125 mM NaCl), and wash C (wash A but with 175 mM NaCl). Bound nucleosomes were washed one last time with TE buffer containing 50 mM NaCl before being eluted with 300 μl elution buffer. RNAase was added to digest RNA for 2 h and Proteinase K to digest proteins for another 2 h at 37oC. DNA (from IP and Input samples) was precipitated and cleaned-up with phenol/chloroform/isomylalcohol and Qiagen clean-up columns. DNA concentration was estimated by Qubit fluorometry and libraries were prepared using the Illumina's TruSeq ChIP Sample Prep Kit (Low Throughput) according to the manufacture's protocol. Libraries were multiplexed 12 per lane on a HiSeq2500 Illumina sequencing machine and sequenced in paired-end mode using the TruSeq Rapid SBS kit

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
27308180
Reads aligned (%)
98.6
Duplicates removed (%)
1.4
Number of peaks
970 (qval < 1E-05)

hg19

Number of total reads
27308180
Reads aligned (%)
97.6
Duplicates removed (%)
2.4
Number of peaks
346 (qval < 1E-05)

Base call quality data from DBCLS SRA