FACS-based isolation of fixed mouse neuronal nuclei for ATAC-seq and Hi-C

Ekaterina Eremenko; Anastasia Golova; Daniel Stein; Monica Einav; Ekaterina Khrameeva; Debra Toiber

doi:10.1016/j.xpro.2021.100643

FACS-based isolation of fixed mouse neuronal nuclei for ATAC-seq and Hi-C

Ekaterina Eremenko, Anastasia Golova, Daniel Stein, Monica Einav, Ekaterina Khrameeva, Debra Toiber

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

The organization of chromatin structure plays a crucial role in gene expression, DNA replication, and repair. Chromatin alterations influence gene expression, and modifications could be associated with genomic instability in the cells during aging or diseases. Here, we provide a modified protocol to isolate fixed neuronal nuclei from a single mouse cortex to investigate the spatial organization of chromatin structure on a genome-wide scale by ATAC-seq (the assay for transposase-accessible chromatin with high-throughput sequencing) and chromatin conformation by Hi-C (high-throughput chromosome conformation capture).

Original language	English
Article number	100643
Journal	STAR Protocols
Volume	2
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2021.100643
State	Published - 17 Sep 2021

Keywords

Cell Biology
Cell separation/fractionation
Flow Cytometry/Mass Cytometry
Genomics
Neuroscience

ASJC Scopus subject areas

General Neuroscience
General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology

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10.1016/j.xpro.2021.100643

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title = "FACS-based isolation of fixed mouse neuronal nuclei for ATAC-seq and Hi-C",

abstract = "The organization of chromatin structure plays a crucial role in gene expression, DNA replication, and repair. Chromatin alterations influence gene expression, and modifications could be associated with genomic instability in the cells during aging or diseases. Here, we provide a modified protocol to isolate fixed neuronal nuclei from a single mouse cortex to investigate the spatial organization of chromatin structure on a genome-wide scale by ATAC-seq (the assay for transposase-accessible chromatin with high-throughput sequencing) and chromatin conformation by Hi-C (high-throughput chromosome conformation capture).",

keywords = "Cell Biology, Cell separation/fractionation, Flow Cytometry/Mass Cytometry, Genomics, Neuroscience",

author = "Ekaterina Eremenko and Anastasia Golova and Daniel Stein and Monica Einav and Ekaterina Khrameeva and Debra Toiber",

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AU - Eremenko, Ekaterina

AU - Golova, Anastasia

AU - Stein, Daniel

AU - Einav, Monica

AU - Khrameeva, Ekaterina

AU - Toiber, Debra

PY - 2021/9/17

Y1 - 2021/9/17

N2 - The organization of chromatin structure plays a crucial role in gene expression, DNA replication, and repair. Chromatin alterations influence gene expression, and modifications could be associated with genomic instability in the cells during aging or diseases. Here, we provide a modified protocol to isolate fixed neuronal nuclei from a single mouse cortex to investigate the spatial organization of chromatin structure on a genome-wide scale by ATAC-seq (the assay for transposase-accessible chromatin with high-throughput sequencing) and chromatin conformation by Hi-C (high-throughput chromosome conformation capture).

AB - The organization of chromatin structure plays a crucial role in gene expression, DNA replication, and repair. Chromatin alterations influence gene expression, and modifications could be associated with genomic instability in the cells during aging or diseases. Here, we provide a modified protocol to isolate fixed neuronal nuclei from a single mouse cortex to investigate the spatial organization of chromatin structure on a genome-wide scale by ATAC-seq (the assay for transposase-accessible chromatin with high-throughput sequencing) and chromatin conformation by Hi-C (high-throughput chromosome conformation capture).

KW - Cell Biology

KW - Cell separation/fractionation

KW - Flow Cytometry/Mass Cytometry

KW - Genomics

KW - Neuroscience

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SN - 2666-1667

VL - 2

JO - STAR Protocols

JF - STAR Protocols

IS - 3

M1 - 100643

ER -

FACS-based isolation of fixed mouse neuronal nuclei for ATAC-seq and Hi-C

Abstract

Keywords

ASJC Scopus subject areas

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