Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR2C2

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
GM12878
biomaterial_provider
GM12878
lab
USC
lab description
Farnham - University of Southern California
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
GM12878
cell organism
human
cell description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
cell karyotype
normal
cell lineage
mesoderm
cell sex
F
treatment
None
treatment description
No special treatment or protocol applies
antibody
TR4
antibody antibodydescription
Rabbit polyclonal. Antibody Target: TR4
antibody targetdescription
(Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus.
antibody vendorname
Donated by Dr. J.D.Engel, University of Michigan
antibody vendorid
TR4
control
std
control description
Standard input signal for most experiments.
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEH000625
labversion
Fragmented using Bioruptor, precipitated with StaphA PeakSeq 1.0 (fdr 0.001), samples were 71% and 72% matching in the top 40% overlap analysis.
replicate
1

Sequenced DNA Library

library_name
GSM935480: USC_ChipSeq_GM12878_TR4_std
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
53708671
Reads aligned (%)
71.5
Duplicates removed (%)
3.1
Number of peaks
2029 (qval < 1E-05)

hg38

Number of total reads
53708671
Reads aligned (%)
72.7
Duplicates removed (%)
2.2
Number of peaks
2036 (qval < 1E-05)

Base call quality data from DBCLS SRA