Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
Glioblastoma
MeSH Description
A malignant form of astrocytoma histologically characterized by pleomorphism of cells, nuclear atypia, microhemorrhage, and necrosis. They may arise in any region of the central nervous system, with a predilection for the cerebral hemispheres, basal ganglia, and commissural pathways. Clinical presentation most frequently occurs in the fifth or sixth decade of life with focal neurologic signs or seizures.

Attributes by original data submitter

Sample

source_name
Gliobla
biomaterial_provider
Dr. Darrell Bigner at Duke University Medical Center
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
treatment
None
treatment description
No special treatment or protocol applies
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
controlid
wgEncodeEH001129
labversion
baseAlignCounts.pl v 1,fseq v 1.84, iff_H54,p-value cutoff: 0.05
replicate
1,2
antibody antibodydescription
rabbit polyclonal
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
controlid
Gliobla/Input
labversion
align_on_cluster_bwa.pl v 1
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM822303: UT-A_ChipSeq_Gliobla_CTCF
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
112388874
Reads aligned (%)
58.6
Duplicates removed (%)
37.7
Number of peaks
70270 (qval < 1E-05)

hg38

Number of total reads
112388874
Reads aligned (%)
60.0
Duplicates removed (%)
36.5
Number of peaks
70959 (qval < 1E-05)

Base call quality data from DBCLS SRA