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-21N
cell type
neuroblastoma cell line
input
SHEP21_24HR_INPUT
treatment
0.2 ug/mL DOX for 24HR
growth condition
10% Tet-Free FBS, RPMI
barcode
TGACCA
chip antibody
MYCN
chip antibody vendor
abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Rx was performed as described previously substituting mouse embryonic stem cells in place of Drosophila S2 cells (Orlando et al., 2014). Mouse embryonic stem (ES) cells were grown to 75% confluence and cross-linked with 1% formaldehyde followed by quenching (125 mM glycine) as described in the previous section. Cells were washed in cold PBS and harvested by cell scraper in cold PBS with protease inhibitors (Roche). Cells were centrifuged at 1650 x g for 5 minutes and flash frozen and stored at -80°C 10E06 cells per pellet. Fixed mouse ES cell pellets were resuspended in a cytosolic lysis buffer and then spiked directly into the cytosolic lysate of fixed neuroblastoma cells at a ratio of 5% of the total number of cells. The lysate (neuroblastoma cells spiked with mouse ES cells) was then carried through the ChIP protocol. 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
104249144
Reads aligned (%)
2.1
Duplicates removed (%)
91.9
Number of peaks
178 (qval < 1E-05)

hg38

Number of total reads
104249144
Reads aligned (%)
2.4
Duplicates removed (%)
91.1
Number of peaks
224 (qval < 1E-05)

Base call quality data from DBCLS SRA