Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CASZ1

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
SMS-CTR cells
cell type
Rhabdomyosarcoma
genotype
stably transfected with CASZ1b, Dox inducible
dox status
No dox
chip antibody
CASZ1 (in collaboration with Rockland, ab8540)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit. Libraries were prepared according to Illumina's TruSeq ChIP Sample Preparation Guide.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
29917174
Reads aligned (%)
87.4
Duplicates removed (%)
8.6
Number of peaks
791 (qval < 1E-05)

hg38

Number of total reads
29917174
Reads aligned (%)
88.4
Duplicates removed (%)
8.0
Number of peaks
670 (qval < 1E-05)

Base call quality data from DBCLS SRA