Protocol for assay of transposase accessible chromatin sequencing in non-model species

Stephen Kissane; Vignesh Dhandapani; Luisa Orsini

doi:10.1016/j.xpro.2021.100341

Protocol for assay of transposase accessible chromatin sequencing in non-model species

STAR Protoc. 2021 Feb 13;2(1):100341. doi: 10.1016/j.xpro.2021.100341. eCollection 2021 Mar 19.

Authors

Stephen Kissane¹, Vignesh Dhandapani¹, Luisa Orsini¹

Affiliation

¹ School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.

Abstract

The assay for transposase accessible chromatin (ATAC-seq) is a method for mapping genome-wide chromatin accessibility. Coupled with high-throughput sequencing, it enables integrative epigenomics analyses. ATAC-seq requires direct access to cell nuclei, a major challenge in non-model species such as small invertebrates, whose soft tissue is surrounded by a protective exoskeleton. Here, we present modifications of the ATAC-seq protocol for applications in small crustaceans, extending applications to non-model species. For complete information on the use and execution of this protocol, please refer to Buenrostro et al. (2013).

Keywords: Bioinformatics; Genomics; High-throughput screening; Sequencing.

Publication types

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

MeSH terms

Animals
Chromatin / genetics*
Chromatin Immunoprecipitation Sequencing*
Chromosome Mapping*
Daphnia / genetics*
Transposases / chemistry*

Substances

Chromatin
Transposases