Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRCA1

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
Osteosarcoma U2OS
cell line
U2OS
cell type
Osteosarcoma
treatment agent
6μM Etoposide for 6 hours
chip antibody
BRCA1 (Santa Cruz, Cat# sc-646)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA was extracted from sub-confluent dishes, fixed and sheared to an average length of 200-1500bp. 10% of the samples from each cell line were pooled to form the Input. RNAPII/BRCA1 antibody was used for immunoprecipitation. ChIP DNA was purified, sheared further to an average length of 350 bp and sequenced after library construction. Sequencing library was prepared using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
60236731
Reads aligned (%)
99.8
Duplicates removed (%)
12.0
Number of peaks
1469 (qval < 1E-05)

hg38

Number of total reads
60236731
Reads aligned (%)
99.9
Duplicates removed (%)
11.7
Number of peaks
1439 (qval < 1E-05)

Base call quality data from DBCLS SRA