Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
NT2-D1
Tissue
testis
Lineage
inner cell mass
Description
malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356)

Attributes by original data submitter

Sample

source_name
embryonal carcinoma cell line
cell line
NT2/D1
cell type
pluripotent embryonal carcinoma cell line
genotype/variation
CRISPR/Cas9-mediated deletion of PRMT6
atra
-
chip antibody
H3K4me3 (07-473, Merck Millipore)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked in the presence of 1% formaldehyde. Cell lysates were sonicated and Protein-DNA complexes were enriched by immunoprecipitation with mentioned antibodies. Libraries were prepared according to the manufacturer's protocol (Diagenode, MicroPlex Library Preparation Kit).

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
34181244
Reads aligned (%)
97.0
Duplicates removed (%)
11.1
Number of peaks
28531 (qval < 1E-05)

hg19

Number of total reads
34181244
Reads aligned (%)
96.5
Duplicates removed (%)
11.8
Number of peaks
28339 (qval < 1E-05)

Base call quality data from DBCLS SRA