Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZMYND11

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
cell type
U2OS Cells
genotype/variation
WT
chip antibody
ZMYND11, home-made

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA seq, total RNA was extracted using QiaGen RNAplus kit. ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. Library was contracted by the MD Anderson DNA sequencing Core facility following standard protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
70817078
Reads aligned (%)
84.1
Duplicates removed (%)
5.7
Number of peaks
1581 (qval < 1E-05)

hg38

Number of total reads
70817078
Reads aligned (%)
86.7
Duplicates removed (%)
3.8
Number of peaks
1597 (qval < 1E-05)

Base call quality data from DBCLS SRA