Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYCN

Cell type

Cell type Class
Neural
Cell type
KELLY
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Kelly neuroblastoma cells
chip antibody
B8.4b (Santa Cruz, Catalog# sc-53993, Lot# K1315)
cell line
Kelly
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
66919424
Reads aligned (%)
33.3
Duplicates removed (%)
19.6
Number of peaks
33985 (qval < 1E-05)

hg38

Number of total reads
66919424
Reads aligned (%)
33.9
Duplicates removed (%)
18.7
Number of peaks
34141 (qval < 1E-05)

Base call quality data from DBCLS SRA