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
MYCN3 cells
cell type
Neuroblastoma cell line with inducible MYCN expression
cell line
MYCN3 (SHEP-MYCN-TET)
antibody
MYCN
condition
mycn-high

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. Chromatin immunoprecipitated DNA was prepared for sequencing following a modified version of Illumina's Genomic DNA protocol. Sheared DNA fragments undergo end repair by T4 DNA polymerase to fill in 5′ overhangs, Klenow polymerase to remove 3′ overhangs, and T4PNK to phosphorylate the 5′-OH. For Illumina adapter ligation, a single adenine nucleotide overhang must be added to the polished DNA. A 1:30 dilution of the Adaptor Oligo Mix (20) was used in the ligation step. The resulting adapted constructs are amplified by 18 cycles of PCR enriching the DNA fragments with adapters flanking each end. The amplified product was quantified using a spectrophotometer at 260 nm (Nanodrop) then a portion of final sample is size separated on a 6% TBE (Invitrogen) to verify correct target range amplification. The validated DNA library is submitted at a 10 nmol/L concentration for sequencing. All protocols for Illumina library sequence preparation, sequencing, and quality control are provided by Illumina.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
3780336
Reads aligned (%)
67.2
Duplicates removed (%)
6.3
Number of peaks
2214 (qval < 1E-05)

hg38

Number of total reads
3780336
Reads aligned (%)
67.9
Duplicates removed (%)
5.9
Number of peaks
2210 (qval < 1E-05)

Base call quality data from DBCLS SRA