Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYCN

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
Neuroblastoma
cell line
SHEP with tetracycline inducible MYCN
input
SHEP_INPUT
treatment
0.2ug/ml doxycycline
growth protocol
10% Tet-Free FBS, RPMI
barcode
TGGTTGTT
chip antibody
MYCN
chip antibody vendor
abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
38140960
Reads aligned (%)
32.4
Duplicates removed (%)
66.4
Number of peaks
3714 (qval < 1E-05)

hg38

Number of total reads
38140960
Reads aligned (%)
33.6
Duplicates removed (%)
65.4
Number of peaks
3609 (qval < 1E-05)

Base call quality data from DBCLS SRA