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

genetic knockout of ASCL1 overexpressing ASCL1

tissue

glioblastoma tumor

derived cell line

G523NS

genotype

knockout ASCL1

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

50,000 cells were lysed for nuclei and was incubated with transposase reaction mix for 30 min at 37 degrees. Libraries were prepared according to Nextera DNA Sample Prep kit. Briefly, library fragments were amplified using 1x NEBnext PCR master mix. Libraries were purified using Qiagen PCR cleanip kit. Libraries were amplified for a total of 13 cycles. Libraries were selected for 240-360bp size fragments.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

43245298

Reads aligned (%)

98.4

Duplicates removed (%)

35.6

Number of peaks

17603 (qval < 1E-05)

hg19

Number of total reads

43245298

Reads aligned (%)

97.9

Duplicates removed (%)

36.4

Number of peaks

17572 (qval < 1E-05)