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 stem cells
cell type
NT2D1
passages
p37
genotype
46 XY +complex
chip antibody
anti-H3K4me3 (C15410003, Diagenode)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Qiagen all prep for smallRNA (S7-13) and mRNA (S1-6), ChIP-DNA (S14-18): Qiagen MinElute PCR Purification Kit smallRNA-seq (S7-13): Illumina TruSeq smallRNA, mRNA-seq (S1-6): Illumina TruSeq mRNA, ChIP-seq (S14-18): Diagenode Microplex Library Preparation kit v2

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg38

Number of total reads
25452774
Reads aligned (%)
99.4
Duplicates removed (%)
22.0
Number of peaks
29669 (qval < 1E-05)

hg19

Number of total reads
25452774
Reads aligned (%)
99.2
Duplicates removed (%)
22.2
Number of peaks
29498 (qval < 1E-05)

Base call quality data from DBCLS SRA