Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

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
Stanford
lab description
Snyder - Stanford University
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
CTCF_(SC-15914)
antibody antibodydescription
Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target: CTCF
antibody targetdescription
Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-15914
control
std
control description
Standard input signal for most experiments.
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEH000625
replicate
1

Sequenced DNA Library

library_name
GSM935611: Stanford_ChipSeq_GM12878_CTCF_(SC-15914)_std
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
45896595
Reads aligned (%)
69.3
Duplicates removed (%)
23.6
Number of peaks
64532 (qval < 1E-05)

hg38

Number of total reads
45896595
Reads aligned (%)
70.4
Duplicates removed (%)
23.0
Number of peaks
60610 (qval < 1E-05)

Base call quality data from DBCLS SRA