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
RD
cell line
RD
chip antibody
MyoD, Santa Cruz (cat sc-32758, lot I1113)
enrichment target
MYOD
mechanistic classifications of chip protein target
Myogenic Transcription Factor
treatment
shSNAI2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
[harvesting protocol] ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit). ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen). DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol. Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
43166723
Reads aligned (%)
71.8
Duplicates removed (%)
11.5
Number of peaks
11274 (qval < 1E-05)

hg38

Number of total reads
43166723
Reads aligned (%)
72.7
Duplicates removed (%)
10.8
Number of peaks
11385 (qval < 1E-05)

Base call quality data from DBCLS SRA