Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

Noga Korenfeld, Nicolaj I. Toft, Trine V. Dam, Meital Charni-Natan, Lars Grøntved*, Ido Goldstein*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.

Original languageAmerican English
Article number102462
JournalSTAR Protocols
Volume4
Issue number3
DOIs
StatePublished - 15 Sep 2023

Bibliographical note

Publisher Copyright:
© 2023 The Author(s)

Keywords

  • Genomics
  • Metabolism
  • Molecular Biology
  • Single Cell

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