Antigen

Antigen Class

Input control

Antigen

Input control

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

NT2/D1_RA_input

cell line

NT2/D1

cell type

embryonal carcinoma cells

treated with

10 μM all trans retinoic acid for 6 days

chip anibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP was performed with ChIP-IT Express Enzymatic kit (Active motif) according to the manufacturer's instructions with some modifications. Briefly, cells were fixed with 1% formaldehyde for 10 min at room temperature. After enzymatic chromatin digestion, we performed sonication (5X30 sec) using the Bioruptor (Diagenode). ChIP-seq libraries were constructed with NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

19317294

Reads aligned (%)

87.5

Duplicates removed (%)

2.4

Number of peaks

682 (qval < 1E-05)

hg19

Number of total reads

19317294

Reads aligned (%)

86.6

Duplicates removed (%)

3.5

Number of peaks

535 (qval < 1E-05)