Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Neural
Cell type
IMR-5/75
NA
NA

Attributes by original data submitter

Sample

source_name
IMR5-75-shMYCN-MYCN high
cell type
neuroblastoma cell line with stable tet-inducible MYCN knockdown (shRNA), minus tet
chip antibody
H3K4me1
chip antibody catalog/vender
ab8895 (Abcam, Cambridge, UK)

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 H3K4me1 (ab8895, Abcam, Cambridge, UK), 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
24394862
Reads aligned (%)
98.4
Duplicates removed (%)
4.4
Number of peaks
39050 (qval < 1E-05)

hg19

Number of total reads
24394862
Reads aligned (%)
98.2
Duplicates removed (%)
4.5
Number of peaks
38817 (qval < 1E-05)

Base call quality data from DBCLS SRA