Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Neuroblastoma
MeSH Description
A common neoplasm of early childhood arising from neural crest cells in the sympathetic nervous system, and characterized by diverse clinical behavior, ranging from spontaneous remission to rapid metastatic progression and death. This tumor is the most common intraabdominal malignancy of childhood, but it may also arise from thorax, neck, or rarely occur in the central nervous system. Histologic features include uniform round cells with hyperchromatic nuclei arranged in nests and separated by fibrovascular septa. Neuroblastomas may be associated with the opsoclonus-myoclonus syndrome. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, pp2099-2101; Curr Opin Oncol 1998 Jan;10(1):43-51)

Attributes by original data submitter

Sample

source_name
Th-MYCN mouse
tissue
superior cervical ganglia
input
NONE
treatment
None
strain
Th-MYCN
barcode
TGGTTGTT
chip antibody
NA
chip antibody vendor
NA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP, tumors and ganglia were immediately flash frozen in liquid nitrogen and stored at -80°C. For immunohistochemistry, tumor and ganglia tissue were immediately fixed in 4% paraformaldehyde before being processed. Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
55700725
Reads aligned (%)
94.7
Duplicates removed (%)
10.6
Number of peaks
35744 (qval < 1E-05)

mm9

Number of total reads
55700725
Reads aligned (%)
94.6
Duplicates removed (%)
10.6
Number of peaks
33333 (qval < 1E-05)

Base call quality data from DBCLS SRA