An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons

Maya Maor-Nof; Zohar Shipony; Georgi K Marinov; William J Greenleaf; Aaron D Gitler

doi:10.1016/j.xpro.2021.100854

An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons

STAR Protoc. 2021 Sep 30;2(4):100854. doi: 10.1016/j.xpro.2021.100854. eCollection 2021 Dec 17.

Authors

Maya Maor-Nof¹, Zohar Shipony¹, Georgi K Marinov¹, William J Greenleaf^{1

2

3

4}, Aaron D Gitler¹

Affiliations

¹ Department of Genetics, Stanford University, Stanford, CA 94305, USA.
² Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
³ Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
⁴ Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.

Abstract

ATAC-seq is a versatile, adaptable, and widely adopted technique for mapping open chromatin regions. However, some biological systems, such as primary neurons, present unique challenges to its application. Conventional ATAC-seq would require the dissociation of the primary neurons after plating but dissociating them leads to rapid cell death and major changes in cell state, affecting ATAC-seq results. We have developed this modified ATAC-seq protocol to address this challenge for primary neurons, providing a high-quality and high-resolution accessible chromatin profile. For complete details on the use and execution of this protocol, please refer to Maor-Nof et al. (2021).

Keywords: Genetics; Genomics; Molecular Biology; Neuroscience; Sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromatin / genetics
Chromatin Immunoprecipitation Sequencing*
High-Throughput Nucleotide Sequencing* / methods
Mice
Neurons
Sequence Analysis, DNA / methods

Substances

Chromatin

Abstract

Publication types

MeSH terms

Substances

Grants and funding