Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
BE(2)-C
Primary Tissue
Brain
Site of Extraction
Bone Marrow
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
BE2_C
biomaterial_provider
ATCC
lab
UW
lab description
Stamatoyannopoulous - University of Washington
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
BE2_C
cell organism
human
cell description
neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.
cell karyotype
cancer
cell lineage
ectoderm
cell sex
M
antibody
CTCF
antibody antibodydescription
Rabbit polyclonal. Antibody Target: CTCF
antibody targetdescription
CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname
Millipore
antibody vendorid
07-729
treatment
None
treatment description
No special treatment or protocol applies
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEH001892
labexpid
DS18308
labversion
Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75
replicate
2

Sequenced DNA Library

library_name
GSM1022650: UW_ChipSeq_BE2_C_CTCFRep2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
25474624
Reads aligned (%)
89.9
Duplicates removed (%)
7.9
Number of peaks
42110 (qval < 1E-05)

hg38

Number of total reads
25474624
Reads aligned (%)
91.5
Duplicates removed (%)
6.9
Number of peaks
42230 (qval < 1E-05)

Base call quality data from DBCLS SRA