Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
Be(2)-C
cell type
neuroblastoma cell line
chip antibody
none

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 antibodies. Antibodies against H3K27ac (ab4729), H3K4me3 (ab8580, Abcam) and H3K27me3 (ab6002, Abcam) were used for precipitation. Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, US) according to the manufacturer’s protocol. Libraries were sequenced (50 bases single-end) on the Illumina sequencing platform (German Cancer Research Center Core facility).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
24208721
Reads aligned (%)
98.8
Duplicates removed (%)
4.1
Number of peaks
1127 (qval < 1E-05)

hg19

Number of total reads
24208721
Reads aligned (%)
98.1
Duplicates removed (%)
5.4
Number of peaks
1210 (qval < 1E-05)

Base call quality data from DBCLS SRA