Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
YY1

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
Chromatin IP Sequencing
cell
NT2-D1
cell organism
human
cell 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)
cell karyotype
cancer
cell lineage
inner cell mass
cell sex
M
treatment
None
treatment description
No special treatment or protocol applies
antibody
YY1
antibody antibodydescription
Rabbit polyclonal. Antibody Target: YY1
antibody targetdescription
YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins.
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-1703
control
UCDavis
control description
Input library was prepared at UC Davis.
control
UCDavis
control description
Input library was prepared at UC Davis.
controlid
wgEncodeEH000654
labversion
Fragmented using Bioruptor, precipitated with StaphA
replicate
1
softwareversion
PeakSeq1.0 (fdr 0.001)

Sequenced DNA Library

library_name
GSM935424: USC_ChipSeq_NT2-D1_YY1_UCDavis
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
45609536
Reads aligned (%)
43.2
Duplicates removed (%)
3.7
Number of peaks
8068 (qval < 1E-05)

hg38

Number of total reads
45609536
Reads aligned (%)
44.1
Duplicates removed (%)
2.6
Number of peaks
8093 (qval < 1E-05)

Base call quality data from DBCLS SRA