Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYCN

Cell type

Cell type Class
Neural
Cell type
SK-N-BE(2)
Primary Tissue
Brain
Site of Extraction
Bone Marrow
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Neuroblastoma cells
biomaterial_provider
ATCC
cell line
SK-N-BE(2)-C
cell type
neuroblastoma
chip antibody
MYCN (Abcam ab16898)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP assay was performed using the EZ-Magna ChIPTM A (Upstate-Millipore, Billerica, MA, USA). Cells were cross-linked in 1% formaldehyde (Sigma-Aldrich, St Louis, MO, USA) for 30 minutes. Nuclear lysates were extracted and the chromatin fraction was sheared to 200- to 500-bp fragments using an ultrasonic probe (Labsonic M, Sartorius, Tagelswangen, Switzerland). Immunoprecipitations were performed using 1 μg of anti-MYCN antibody (Abcam, Cambridge, UK) or 1 μg of anti-mouse IgG1κ antibody (Abcam) as control overnight at 4°C. After washed off unspecific DNA binding, the protein/DNA complexes were eluted and reverse corsslinked to free DNA fragments as described in manual. Purified fragmented DNA was subjected to ChIP-seq analysis for determining MYCN binding regions. Then DNA fragments 150–400 bp long were gel purified following the adaptor ligation step. The PCR-amplified DNA libraries were quantified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and diluted for cluster generation. The ChIP-seq libraries assayed by single-end sequencing on an Illumina HiSeq platform sequencing in Beijing Genomics Institute (BGI).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
12000000
Reads aligned (%)
85.8
Duplicates removed (%)
12.3
Number of peaks
498 (qval < 1E-05)

hg38

Number of total reads
12000000
Reads aligned (%)
87.6
Duplicates removed (%)
11.0
Number of peaks
260 (qval < 1E-05)

Base call quality data from DBCLS SRA