Antigen

Antigen Class

Histone

Antigen

H3K27me3

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

Glioblastoma initiating cells

genotype/variation

PTEN-/-;p53-/-

cell type

Glioblastoma initiating cells

chip antibody

anti-H3K27me3

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin was extracted and sonicated to get fragments of 100 to 500 bp, then immunoprecipitated with 10 µL of anti-H3K27me3 (Active Motif, #39155). ChIPSeq libraries were prepared following the Illumina protocol and ligated to standard PE adaptors and sequenced on a HiSeq2000. Total RNA was extracted using Mini RNeasy kit (Qiagen) according to the manufacturer's instructions. For RNASeq, 200 ng of total RNA was used to prepare RNASeq libraries using the TruSeq RNA kit from Illumina following the instructions provided in the supplier's manual, and sequenced on HiSeq2000.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

17992694

Reads aligned (%)

83.5

Duplicates removed (%)

27.5

Number of peaks

451 (qval < 1E-05)

mm9

Number of total reads

17992694

Reads aligned (%)

83.0

Duplicates removed (%)

27.4

Number of peaks

1278 (qval < 1E-05)