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
GBM3565
tissue
glioblastoma patient-derived cell model
chip antibody
rabbit anti-CTCF (Cell Signaling #3418)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according previous methods (e.g. Schmidt et al. Methods 2009). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina MiSeq 500 following the manufacturer's protocols using 75 bp single end reads.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg19

Number of total reads
137618864
Reads aligned (%)
153.6
Duplicates removed (%)
16.2
Number of peaks
30411 (qval < 1E-05)

hg38

Number of total reads
137618864
Reads aligned (%)
155.8
Duplicates removed (%)
15.6
Number of peaks
33691 (qval < 1E-05)

Base call quality data from DBCLS SRA