Antigen

Antigen Class

Unclassified

Antigen

Unclassified

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.

Sample

source_name

primary GBM cell culture

culture

G567

digestion protocol

MNase digest

tissue

primary glioblastoma

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were either treated with media containing 1% formaldehyde for 10 minutes at room temperature followed by quenching, wash and snap-freezing (CTCF) or by snap-freezing of native samples (H3K27Ac).Chromatin from 3 million cells was used to perform ChIP with 1 uL of CTCF antibody (CST #3418; lot 1) or with 1 ug of H3K27Ac antibody (Active Motif #39133, lot # 31814008) Libraries were size selected and amplified using the NEBNext Ultra II DNA kit (New England Biolabs).

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

43368782

Reads aligned (%)

96.9

Duplicates removed (%)

24.9

Number of peaks

45187 (qval < 1E-05)

hg19

Number of total reads

43368782

Reads aligned (%)

96.6

Duplicates removed (%)

25.0

Number of peaks

45567 (qval < 1E-05)