Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

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 type
Cell line derived from a bone cancer patient
cell line
U2OS
chip antibody
H3K9me3
treatment
ORCA knockdown

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde (Sigma) was added to culture medium to a final concentration of 1%. Crosslinking was allowed to proceed for 10 min at room temperature and stopped by addition of glycine at a final concentration of 0.125 M. Fixed cells were washed and harvested with PBS. Chromatin was prepared by two subsequent extraction steps (10 min at 4°C) with Buffer 1 (50 mM Hepes/KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton) and Buffer 2 (200 mM NaCl; 1mM EDTA; 0.5mM EGTA; 10 mM Tris pH 8). Nuclei were then pelleted by centrifugation, resuspended in Buffer 3 (50 mM Tris pH 8; 0.1% SDS; 1% NP-40; 0.1% Na-Deoxycholate; 10 mM EDTA; 150 mM NaCl) and subjected to sonication with Bioruptor Power-up (Diagenode) yealding genomic DNA fragments with a bulk size of 150-300 bp. The ChIPseq libraries were prepared with Illumina's 'TruSeq DNA Sample Prep kit'.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
28771670
Reads aligned (%)
95.6
Duplicates removed (%)
3.0
Number of peaks
1244 (qval < 1E-05)

hg19

Number of total reads
28771670
Reads aligned (%)
94.3
Duplicates removed (%)
5.0
Number of peaks
890 (qval < 1E-05)

Base call quality data from DBCLS SRA