Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYOD1

Cell type

Cell type Class
Muscle
Cell type
Rhabdomyosarcoma
MeSH Description
A malignant solid tumor arising from mesenchymal tissues which normally differentiate to form striated muscle. It can occur in a wide variety of sites. It is divided into four distinct types: pleomorphic, predominantly in male adults; alveolar (RHABDOMYOSARCOMA, ALVEOLAR), mainly in adolescents and young adults; embryonal (RHABDOMYOSARCOMA, EMBRYONAL), predominantly in infants and children; and botryoidal, also in young children. It is one of the most frequently occurring soft tissue sarcomas and the most common in children under 15. (From Dorland, 27th ed; Holland et al., Cancer Medicine, 3d ed, p2186; DeVita Jr et al., Cancer: Principles & Practice of Oncology, 3d ed, pp1647-9)

Attributes by original data submitter

Sample

source_name
Rhabdomyosarcoma
tissue
Rhabdomyosarcoma
chip antibody
MyoD

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Primary myoblast samples were collected in growth medium at low density, and both primary myotubes and RD cells were collected after being cultured in differentiation medium (72 h for myotubes, 24 h for RD cells). Libraries were generated from immunoprecipitated DNA as outlined in the Illumina DNA Library Construction Kit protocol except that 21 rounds of PCR were performed for amplification, and DNA fragments ranging from 200-350 bp were isolated during size selection on agarose gel.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
14195789
Reads aligned (%)
87.9
Duplicates removed (%)
6.1
Number of peaks
32501 (qval < 1E-05)

hg38

Number of total reads
14195789
Reads aligned (%)
88.9
Duplicates removed (%)
5.6
Number of peaks
32472 (qval < 1E-05)

Base call quality data from DBCLS SRA