Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Bone
Cell type
Osteosarcoma
MeSH Description
A sarcoma originating in bone-forming cells, affecting the ends of long bones. It is the most common and most malignant of sarcomas of the bones, and occurs chiefly among 10- to 25-year-old youths. (From Stedman, 25th ed)

Attributes by original data submitter

Sample

source_name
Osteosarcoma cells
tissue
bone
disease
osteosarcoma
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
U2-OS and SJSA-1 cells were cultured at 37 °C in 5% CO2, and were cross-linked with 1% formaldehyde at room temperature for 10 min followed by neutralization with glycine. Cells were resuspended, lysed in lysis buffer, and sonicated on ice to shear most DNA to 200-750 bp. Libraries were generated for ChIP samples following the NEBNext® Ultra™DNA Library Prep Kit for Illumina protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
31999467
Reads aligned (%)
92.2
Duplicates removed (%)
8.5
Number of peaks
1562 (qval < 1E-05)

hg19

Number of total reads
31999467
Reads aligned (%)
91.0
Duplicates removed (%)
11.2
Number of peaks
1555 (qval < 1E-05)

Base call quality data from DBCLS SRA