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

Animals Cell Nucleus / genetics Chromatin / genetics Chromatin Immunoprecipitation Sequencing / methods Flow Cytometry / methods High-Throughput Nucleotide Sequencing / methods Mice, Inbred C57BL Neurons / cytology Polymerase Chain Reaction Transposases
Cell Biology Cell separation/fractionation Flow Cytometry/Mass Cytometry Genomics Neuroscience

Journal

STAR protocols
ISSN: 2666-1667
Titre abrégé: STAR Protoc
Pays: United States
ID NLM: 101769501

Informations de publication

Date de publication:
17 09 2021
Historique:
entrez: 26 7 2021
pubmed: 27 7 2021
medline: 27 7 2021
Statut: epublish

Résumé

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).

Identifiants

DOI: 10.1016/j.xpro.2021.100643 PMID: 34308377 PMC: PMC8283150
pubmed: 34308377
doi: 10.1016/j.xpro.2021.100643
pii: S2666-1667(21)00350-6
pmc: PMC8283150
doi:

Substances chimiques

Chromatin 0
Transposases EC 2.7.7.-

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Pagination

100643

Informations de copyright

© 2021 The Author(s).

Déclaration de conflit d'intérêts

The authors declare no competing interests.

Références

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pubmed: 24713002
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Nat Biotechnol. 2020 Mar;38(3):276-278
pubmed: 32055031
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Nat Methods. 2016 Dec;13(12):1013-1020
pubmed: 27749837
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pubmed: 18007629
Methods. 2017 Jul 1;123:56-65
pubmed: 28435001
J Vis Exp. 2016 Aug 27;(114):
pubmed: 27685012

Auteurs

Ekaterina Eremenko (E)

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

Anastasia Golova (A)

Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.

Daniel Stein (D)

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

Monica Einav (M)

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

Ekaterina Khrameeva (E)

Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.

Debra Toiber (D)

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Cellules › Structures cellulaires › Espace intracellulaire › Cytoplasme › Structures cytoplasmiques › Organites › Noyau de la cellule › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Techniques d'investigation › Techniques immunologiques › Immunoprécipitation › Immunoprécipitation de la chromatine › Séquençage après immunoprécipitation de la chromatine › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Techniques d'investigation › Techniques cytologiques › Cytophotométrie › Cytométrie en flux › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › Lignées consanguines de souris › Souris de lignée C57BL › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Cellules › Neurones › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Techniques d'amplification d'acides nucléiques › Réaction de polymérisation en chaîne › FACS-based isolation of fixed mouse neuronal...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Transferases › Phosphotransferases › Nucleotidyltransferases › Transposases › FACS-based isolation of fixed mouse neuronal...