Chromatin Accessibility Profiling and Data Analysis Using ATAC-seq in Nothobranchius furzeri
- 1Department of Genetics, Stanford University, Stanford University, Stanford, California 94305, USA
- 2Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305, USA
- ↵3Correspondence: abrunet1{at}stanford.edu
Abstract
The state of genome-wide chromatin accessibility in cells, tissues, or organisms can be investigated with a technique called assay for transposase-accessible chromatin using sequencing (ATAC-seq). ATAC-seq is a powerful approach for profiling the epigenomic landscape of cells using very low input materials. Analysis of chromatin accessibility data allows for prediction of gene expression and identification of regulatory elements such as potential enhancers and specific transcription-factor binding sites. Here, we describe an optimized ATAC-seq protocol for the preparation of isolated nuclei and subsequent next-generation sequencing from whole embryos and tissues of the African turquoise killifish (Nothobranchius furzeri). Importantly, we provide an overview of a pipeline for processing and analyzing ATAC-seq data from killifish.
Footnotes
-
From the African Turquoise Killifish collection, edited by Anne Brunet.
