Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EP400

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
antibody
anti-EP400 antibody is from Abcam, ab70301
cell line
U2OS

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was extracted with Trizol, digested with DNaseI and further purified by acid phenol. For ChIP-Seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with respective antibodides. Libraries for ChIP-seq were prepared with KAPA LTP kit and RNA-seq Illumina TruSeq RNA Sample Prep Kits v2 according to the manufacturer’s protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
17182068
Reads aligned (%)
84.2
Duplicates removed (%)
6.2
Number of peaks
670 (qval < 1E-05)

hg38

Number of total reads
17182068
Reads aligned (%)
84.9
Duplicates removed (%)
4.6
Number of peaks
487 (qval < 1E-05)

Base call quality data from DBCLS SRA