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
NT2-D1
biomaterial_provider
ATCC
lab
USC
lab description
Farnham - University of Southern California
datatype
ChipSeq
datatype description
ChIP-Seq
cell
NT2-D1
cell organism
human
cell description
malignant pluripotent embryonal carcinoma (Ntera2), "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)
cell karyotype
cancer
cell lineage
inner cell mass
cell sex
M
treatment
None
treatment description
No special treatment or protocol applies
antibody
H3K4me3B
antibody antibodydescription
Rabbit monoclonal antibody
antibody targetdescription
Histone H3 (tri-methyl K4) marks promoters in chromatin regions
antibody vendorname
Cell Signaling
antibody vendorid
9751S
control
UCDavis
control description
Input library was prepared at UC Davis.
control
UCDavis
control description
Input library was prepared at UC Davis.
controlid
wgEncodeEH000654
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM788072: USC_ChipSeq_NT2-D1_H3K4me3B_UCDavis
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
44660086
Reads aligned (%)
72.2
Duplicates removed (%)
4.4
Number of peaks
29931 (qval < 1E-05)

hg19

Number of total reads
44660086
Reads aligned (%)
71.8
Duplicates removed (%)
5.0
Number of peaks
31111 (qval < 1E-05)

Base call quality data from DBCLS SRA