Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

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 (GR alpha)
chip antibody
GR (Santa Cruz)
sirna
siHic5
hormone
100nM dex for 1h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde at room temperature for 1 hour, quenched with 0.125M Glycine and washed with PBS. Chromatin was isolated using a lysis buffer containing 1% SDS, 50 mM Tris-HCl (pH 8.0), and 10 mM EDTA. The chromatin extracts were sonicated for 20 min (in repeated cycles of 30-s on/30-s off) using a Bioruptor (Diagenode) kept at 4 °C with a circulating water bath to achieve a DNA fragment size of 300–400 bp. Standard protocol at Next-Generation Sequencing Core of USC Norris Comprehensive Cancer Center

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
41679100
Reads aligned (%)
97.5
Duplicates removed (%)
11.6
Number of peaks
32630 (qval < 1E-05)

hg38

Number of total reads
41679100
Reads aligned (%)
98.4
Duplicates removed (%)
9.9
Number of peaks
32872 (qval < 1E-05)

Base call quality data from DBCLS SRA