Antigen

Antigen Class

TFs and others

Antigen

MYCN

Cell type

Cell type Class

Neural

Cell type

NGP

NA

NA

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 (%)

61.5

Duplicates removed (%)

12.6

Number of peaks

51448 (qval < 1E-05)

hg38

Number of total reads

87083932

Reads aligned (%)

61.8

Duplicates removed (%)

11.5

Number of peaks

52234 (qval < 1E-05)