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 journalArticlepeer-review

2 Scopus citations


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 languageEnglish
Article number100643
JournalSTAR Protocols
Issue number3
StatePublished - 17 Sep 2021


  • 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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