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
antibody
c-MYC N262 (Santa Cruz, sc764)
sirna treatment
siMYC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq in MYC-induced U2OS cells, libraries from GEO record GSE44672 were used and sequenced deeper. For ChIP-seq in MYC-depleted U2OS cells, 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 Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using phenol-chloroform extraction and ethanol precipitation. 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. 

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
9851380
Reads aligned (%)
83.5
Duplicates removed (%)
36.9
Number of peaks
758 (qval < 1E-05)

hg38

Number of total reads
9851380
Reads aligned (%)
84.1
Duplicates removed (%)
35.6
Number of peaks
679 (qval < 1E-05)

Base call quality data from DBCLS SRA