ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells

Chromatin accessibility is critical for cell identity. Conventional ATAC-seq can examine chromatin accessibility on freshly prepared muscle stem cells or satellite cells (SCs); however, isolating SCs in mice remains challenging. Here, we present a protocol to preserve the in vivo chromatin profile o...

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Detalles Bibliográficos
Autores principales: Dong, Anqi, Chan, Indigo T.C., Cheung, Tom H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320306/
https://www.ncbi.nlm.nih.gov/pubmed/37352103
http://dx.doi.org/10.1016/j.xpro.2023.102376
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author Dong, Anqi
Chan, Indigo T.C.
Cheung, Tom H.
author_facet Dong, Anqi
Chan, Indigo T.C.
Cheung, Tom H.
author_sort Dong, Anqi
collection PubMed
description Chromatin accessibility is critical for cell identity. Conventional ATAC-seq can examine chromatin accessibility on freshly prepared muscle stem cells or satellite cells (SCs); however, isolating SCs in mice remains challenging. Here, we present a protocol to preserve the in vivo chromatin profile of SCs by applying paraformaldehyde (PFA) perfusion throughout the mouse before SC isolation. We describe steps for PFA perfusion and FACS sorting of SCs. We then detail library preparation for ATAC-seq. For complete details on the use and execution of this protocol, please refer to Dong et al.(1)
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spelling pubmed-103203062023-07-06 ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells Dong, Anqi Chan, Indigo T.C. Cheung, Tom H. STAR Protoc Protocol Chromatin accessibility is critical for cell identity. Conventional ATAC-seq can examine chromatin accessibility on freshly prepared muscle stem cells or satellite cells (SCs); however, isolating SCs in mice remains challenging. Here, we present a protocol to preserve the in vivo chromatin profile of SCs by applying paraformaldehyde (PFA) perfusion throughout the mouse before SC isolation. We describe steps for PFA perfusion and FACS sorting of SCs. We then detail library preparation for ATAC-seq. For complete details on the use and execution of this protocol, please refer to Dong et al.(1) Elsevier 2023-06-22 /pmc/articles/PMC10320306/ /pubmed/37352103 http://dx.doi.org/10.1016/j.xpro.2023.102376 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Dong, Anqi
Chan, Indigo T.C.
Cheung, Tom H.
ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells
title ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells
title_full ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells
title_fullStr ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells
title_full_unstemmed ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells
title_short ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells
title_sort atac-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320306/
https://www.ncbi.nlm.nih.gov/pubmed/37352103
http://dx.doi.org/10.1016/j.xpro.2023.102376
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