Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NELFE

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
Human osteosarcoma cell line
cell line
U2OS
cell type
Human osteosarcoma cell line
chip antibody
NELFE, Milipore, Cat# ABE48

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
U2OS cells were cross-linked in medium containing 1% formaldehyde for 10 min at room temperature, neutralized with 0.125 M glycine, scraped off and rinsed twice with PBS. Pellets were resuspended in 10 ml of buffer L1 (50 mM Hepes KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol, 5% NP-40, 0.25% Triton X-100) and incubated for 10 min at 4°C. Cells were spun down, resuspended in 10 ml of buffer L2 (200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 10 mM Tris pH 8.0) and incubated for 10 min at room temperature followed by centrifugation and resuspension in 900 μl buffer L3 (1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 10 mM Tris pH 8.0, 100 mM NaCl, 0.1% Na-deoxycholate, 0.17 mM N-lauroyl sarcosine, supplemented with protease inhibitors). Library was prepared with Ovation Ultralow Library Systems v2 (NuGEN) according to manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
31107733
Reads aligned (%)
97.2
Duplicates removed (%)
13.9
Number of peaks
1366 (qval < 1E-05)

hg38

Number of total reads
31107733
Reads aligned (%)
98.2
Duplicates removed (%)
12.2
Number of peaks
1420 (qval < 1E-05)

Base call quality data from DBCLS SRA