Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

Noga Korenfeld; Nicolaj I Toft; Trine V Dam; Meital Charni-Natan; Lars Grøntved; Ido Goldstein

doi:10.1016/j.xpro.2023.102462

Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

Noga Korenfeld, Nicolaj I Toft, Trine V Dam, Meital Charni-Natan, Lars Grøntved, Ido Goldstein^*

^*Kontaktforfatter

The Hebrew University of Jerusalem

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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Abstract

The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.

Originalsprog	Engelsk
Artikelnummer	102462
Tidsskrift	STAR Protocols
Vol/bind	4
Udgave nummer	3
ISSN	2666-1667
DOI	https://doi.org/10.1016/j.xpro.2023.102462
Status	Udgivet - 15. sep. 2023

Dokumenter og links

10.1016/j.xpro.2023.102462Licens: CC BY-NC-ND

Open Access VersionForlagets udgivne version, 4,58 MBLicens: CC BY-NC-ND

1 Ph.d.-afhandling

Spatial and Temporal Regulation of the Hepatic Chromatin Landscape
Bidragets oversatte titel: Spatial og temporal regulering af det hepatiske kromatin landskabToft, N. I., 7. jun. 2024, Syddansk Universitet. Det Naturvidenskabelige Fakultet. 144 s.
Publikation: Afhandling › Ph.d.-afhandling

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Citationsformater

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AU - Korenfeld, Noga

AU - Toft, Nicolaj I

AU - Dam, Trine V

AU - Charni-Natan, Meital

AU - Grøntved, Lars

AU - Goldstein, Ido

PY - 2023/9/15

Y1 - 2023/9/15

N2 - The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.

AB - The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.

U2 - 10.1016/j.xpro.2023.102462

DO - 10.1016/j.xpro.2023.102462

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Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

Abstract

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Spatial and Temporal Regulation of the Hepatic Chromatin Landscape

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