Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2D

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
NT2D1_KO_KMT2D_+RA
cell line
NT2/D1
cell type
embryonal carcinoma cell line
cell status
pluripotent
genotype/variation
CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells
chip antibody
rabbit (SC-293217, santa cruz)

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 sonified 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

hg19

Number of total reads
32467811
Reads aligned (%)
91.2
Duplicates removed (%)
5.2
Number of peaks
563 (qval < 1E-05)

hg38

Number of total reads
32467811
Reads aligned (%)
92.1
Duplicates removed (%)
4.7
Number of peaks
431 (qval < 1E-05)

Base call quality data from DBCLS SRA