Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
SK-N-SH
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
SK-N-SH
biomaterial_provider
ATCC
lab
Stanford
lab description
Snyder - Stanford University
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
SK-N-SH
cell organism
human
cell description
neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.
cell karyotype
cancer
cell lineage
ectoderm
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
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
control
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
controlid
wgEncodeEH003393

Sequenced DNA Library

library_name
GSM1003633: Stanford_ChipSeq_SK-N-SH_CTCF_(SC-15914)_IgG-rab
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
51629883
Reads aligned (%)
76.1
Duplicates removed (%)
18.1
Number of peaks
52135 (qval < 1E-05)

hg38

Number of total reads
51629883
Reads aligned (%)
77.5
Duplicates removed (%)
17.0
Number of peaks
51470 (qval < 1E-05)

Base call quality data from DBCLS SRA