Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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 cells stably expressing Bmal1:Luc
cell line
osteosarcoma cell line U2OS stably expressing Bmal1:Luc
agent
6AN
chip antibody
anti-H3K4me3 (#39159; Active Motif)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-Seq: Standard RNA extraction with Zymo Direct-zol™ RNA kits. ChIP-Seq: Crosslinked nuclei from U2OS cells were sonicated and protein-DNA complexes were isolated with the following antibodies: anti-CLOCK (NB100-126; Novus Biologicals), anti-BMAL1 (ab3350; Abcam), anti-H3K9ac (ab4441; Abcam) and anti-H3K4me3 (#39159; Active Motif). Illumina TrueSeq platform compatible dual-indexed multiplex library protocol was followed.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
9034949
Reads aligned (%)
88.4
Duplicates removed (%)
13.1
Number of peaks
20575 (qval < 1E-05)

hg19

Number of total reads
9034949
Reads aligned (%)
87.9
Duplicates removed (%)
13.2
Number of peaks
20421 (qval < 1E-05)

Base call quality data from DBCLS SRA