Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Neural

Cell type

Brain

MeSH Description

The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.

Sample

source_name

brain

cell line

Brx50

metastatic site

brain

grown_in_culture

no

dissociation_protocol

braindisso

generation

2

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Nuclei preparation was generated by resuspension of 25,000 or 50,000 sorted cells in nonionic lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA630). Transposition reaction was performed by using the Tn5 transposase (Nextera kit) at 37ºC for 30 minutes. Transposed DNA was further amplified by PCR, and the generated libraries were purified using Agencourt AMPure XP (Beckman Coulter). Library quality was controlled by using a Bioanalyzer high-sensitivity DNA analysis kit (Agilent)

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

43092437

Reads aligned (%)

94.1

Duplicates removed (%)

75.6

Number of peaks

1818 (qval < 1E-05)

hg19

Number of total reads

43092437

Reads aligned (%)

93.9

Duplicates removed (%)

75.7

Number of peaks

1794 (qval < 1E-05)