Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

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, -Dox, Myc ChIP
cell line
U2OS
doxycycline induction
-
chip antibody
anti-c-Myc (N262) [Santa Cruz, catalog# sc764]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-sepharose or Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using Qiagen PCR purification columns. Libraries were constructed following manufacturer's instructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
8770335
Reads aligned (%)
86.0
Duplicates removed (%)
5.6
Number of peaks
1678 (qval < 1E-05)

hg38

Number of total reads
8770335
Reads aligned (%)
87.5
Duplicates removed (%)
4.6
Number of peaks
1562 (qval < 1E-05)

Base call quality data from DBCLS SRA