Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYCN

Cell type

Cell type Class
Neural
Cell type
NGP
NA
NA

Attributes by original data submitter

Sample

source_name
NGP neuroblastoma cells
chip antibody
B8.4b (Santa Cruz, Catalog# sc-53993, Lot# K1315)
cell line
NGP
cell type
Neuroblastoma
mycn status
amplified

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in 5 pellet volumes of FA lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 1.0% Triton-X-100, 0.1% SDS, 0.1% Deoxycholate), supplemented with fresh protease inhibitors and DTT. Beads were washed 3x in ChIP Wash Buffer (0.1% SDS,1.0% Tritotn-X-100, 2mM EDTA pH 8.0, 150mM NaCl, 20mM Tris-HCL pH8.0)and once with Final Wash Buffer (0.1% SDS, 1.0% Triton-X-100, 2mM EDTA pH8.0, 500mM NaCl, 20mM Tris-HCL pH 8.0) NEB Ultra manufacturer's instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
87083932
Reads aligned (%)
53.7
Duplicates removed (%)
12.6
Number of peaks
51448 (qval < 1E-05)

hg38

Number of total reads
87083932
Reads aligned (%)
54.7
Duplicates removed (%)
11.5
Number of peaks
52234 (qval < 1E-05)

Base call quality data from DBCLS SRA