Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

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

Germinal Matrix

cell type

EGFR- cells

gbm classification

NA

gestational stage

19 gestational weeks

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

EGFR+ and EGFR– cell populations were directly isolated from fresh GM and GBM tissues using FACS, without any prior culturing. Upon FACS isolation, cells were collected in 1xPBS and tagmented with Tn5 enzyme (Illumina, FC-121-1030) for 50min and consequently frozen until library construction. DNA was amplified with Custom Nextera PCR Primers cointaining barcodes for 9-14 PCR cycles (NEBNext High-Fidelity 2x PCR Master Mix (New England Labs Cat #M0541). Amplicons were run and extracted from agarose gels with a size selection for 150-700bp fragments in order to optimize yield.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

45411064

Reads aligned (%)

88.9

Duplicates removed (%)

20.3

Number of peaks

41691 (qval < 1E-05)

hg19

Number of total reads

45411064

Reads aligned (%)

88.6

Duplicates removed (%)

20.5

Number of peaks

41524 (qval < 1E-05)