Protocol for isolation and ATAC-seq library construction of zebrafish red blood cells

Yanyan Ding; Feng Liu

doi:10.1016/j.xpro.2022.101889

Protocol for isolation and ATAC-seq library construction of zebrafish red blood cells

STAR Protoc. 2022 Dec 16;3(4):101889. doi: 10.1016/j.xpro.2022.101889. Epub 2022 Nov 23.

Authors

Yanyan Ding¹, Feng Liu²

Affiliations

¹ State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Shandong University, Qingdao, China.
² State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Shandong University, Qingdao, China. Electronic address: liuf@ioz.ac.cn.

Abstract

Understanding chromatin dynamics in red blood cells (RBCs) is critical for exploring the differentiation process and homeostasis maintenance during erythropoiesis. Here, we describe a protocol for isolation of zebrafish erythrocytes labelled with gata1:dsRed by fluorescence-activated cell sorting. We detail steps for ATAC-seq library construction from the isolated RBCs and describe how to analyze the quality of the library. The library can then be used to assay genome-wide chromatin accessibility in these RBCs. For complete details on the use and execution of this protocol, please refer to Ding et al. (2021).¹.

Keywords: Cell Biology; Developmental biology.

Publication types

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

MeSH terms

Animals
Chromatin
Chromatin Immunoprecipitation Sequencing*
Erythrocytes
Sequence Analysis, DNA / methods
Zebrafish* / genetics

Substances

Chromatin