Antigen

Antigen Class

Histone

Antigen

H3K4me1

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)

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

H3K4me1 (39297, Active Motif)

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

31439826

Reads aligned (%)

98.3

Duplicates removed (%)

6.0

Number of peaks

328 (qval < 1E-05)

hg19

Number of total reads

31439826

Reads aligned (%)

97.8

Duplicates removed (%)

6.8

Number of peaks

333 (qval < 1E-05)