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^*

^*Corresponding author for this work

The Hebrew University of Jerusalem

Research output: Contribution to journal › Journal article › Research › 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.

Original language	English
Article number	102462
Journal	STAR Protocols
Volume	4
Issue number	3
ISSN	2666-1667
DOIs	https://doi.org/10.1016/j.xpro.2023.102462
Publication status	Published - 15. Sept 2023

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

Open Access VersionFinal published version, 4.58 MBLicence: CC BY-NC-ND

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1 Ph.D. thesis

Spatial and Temporal Regulation of the Hepatic Chromatin Landscape
Toft, N. I., 7. Jun 2024, Syddansk Universitet. Det Naturvidenskabelige Fakultet. 144 p.
Research output: Thesis › Ph.D. thesis

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title = "Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue",

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.",

author = "Noga Korenfeld and Toft, {Nicolaj I} and Dam, {Trine V} and Meital Charni-Natan and Lars Gr{\o}ntved and Ido Goldstein",

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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

M3 - Journal article

C2 - 37590150

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VL - 4

JO - STAR Protocols

JF - STAR Protocols

IS - 3

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ER -

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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