Antigen

Antigen Class

Histone

Antigen

H3K27ac

Cell type

Cell type Class

Neural

Cell type

Ependymoma

MeSH Description

Glioma derived from EPENDYMOGLIAL CELLS that tend to present as malignant intracranial tumors in children and as benign intraspinal neoplasms in adults. It may arise from any level of the ventricular system or central canal of the spinal cord. Intracranial ependymomas most frequently originate in the FOURTH VENTRICLE and histologically are densely cellular tumors which may contain ependymal tubules and perivascular pseudorosettes. Spinal ependymomas are usually benign papillary or myxopapillary tumors. (From DeVita et al., Principles and Practice of Oncology, 5th ed, p2018; Escourolle et al., Manual of Basic Neuropathology, 2nd ed, pp28-9)

Sample

source_name

Brain

tumor type

Ependymoma

epigenetic mark

H3K27ac

diagnosis

Primary

molecular subgroup

NON-RELA

chip antibody

anti-H3K27ac (Abcam, AB4729, Lot #GR184557)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Upon surgical resection, primary tumors were snap frozen and pulvarized in liquid nitrogen, before proceeding with the ChIP experiment (Mack et al., Nature, 2014) ChIP samples were quantified using Picogreen (Invitrogen) and libraries were constructed using the Rubicon Thruplex DNA-seq kit, according to manufacturers recommendations

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

23940975

Reads aligned (%)

94.9

Duplicates removed (%)

16.2

Number of peaks

19676 (qval < 1E-05)

hg19

Number of total reads

23940975

Reads aligned (%)

94.7

Duplicates removed (%)

16.3

Number of peaks

19612 (qval < 1E-05)