Journal Article

DZNE-2023-01044

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq.

Carraro, C. (First author)DZNE* ; Bonaguro, L.DZNE* ; Srinivasa, R.DZNE* ; van Uelft, M.DZNE* ; Isakzai, V.DZNE* ; Schulte-Schrepping, J.DZNE* ; Gambhir, P.DZNE* ; Elmzzahi, T.DZNE* ; Montgomery, J. V.DZNE* ; Hayer, H.DZNE* ; Li, Y.DZNE* ; Theis, H.DZNE* ; Kraut, M.DZNE* ; Mahbubani, K. T. ; Aschenbrenner, A. C.DZNE* ; König, I.DZNE* ; Fava, E.DZNE* ; Fried, H.-U.DZNE* ; De Domenico, E.DZNE* ; Beyer, M.DZNE* ; Saglam, A.DZNE* ; Schultze, J. L. (Last author)DZNE*

2023
Cell Press Cambridge, MA

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Please use a persistent id in citations: doi:10.1016/j.crmeth.2023.100598

Abstract: Spatially resolved omics technologies reveal context-dependent cellular regulatory networks in tissues of interest. Beyond transcriptome analysis, information on epigenetic traits and chromatin accessibility can provide further insights on gene regulation in health and disease. Nevertheless, compared to the enormous advancements in spatial transcriptomics technologies, the field of spatial epigenomics is much younger and still underexplored. In this study, we report laser capture microdissection coupled to ATAC-seq (LCM-ATAC-seq) applied to fresh frozen samples for the spatial characterization of chromatin accessibility. We first demonstrate the efficient use of LCM coupled to in situ tagmentation and evaluate its performance as a function of cell number, microdissected areas, and tissue type. Further, we demonstrate its use for the targeted chromatin accessibility analysis of discrete contiguous or scattered cell populations in tissues via single-nuclei capture based on immunostaining for specific cellular markers.

Keyword(s): Chromatin: genetics (MeSH) ; Chromatin Immunoprecipitation Sequencing (MeSH) ; Laser Capture Microdissection (MeSH) ; Gene Expression Profiling (MeSH) ; Freezing (MeSH) ; ATAC-seq ; CP: Molecular biology ; chromatin accessibility ; epigenomics ; laser capture microdissection ; spatial omics ; Chromatin

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Contributing Institute(s):

1. Clinical Single Cell Omics (CSCO) / Systems Medicine (AG Schultze)
2. Platform for Single Cell Genomics and Epigenomics (Schultze - PRECISE)
3. Immunogenomics and Neurodegeneration (AG Beyer)
4. Aging and Immunity (AG Aschenbrenner ; AG Aschenbrenner)
5. Light Microscopy Facility (CRFS-LMF) (LMF)
6. Core Research Facilities & Services (AG Fava)

Research Program(s):

1. 352 - Disease Mechanisms (POF4-352) (POF4-352)
2. 354 - Disease Prevention and Healthy Aging (POF4-354) (POF4-354)
3. 351 - Brain Function (POF4-351) (POF4-351)

Experiment(s):

1. Platform for Single Cell Genomics and Epigenomics at DZNE University of Bonn
2. Light Microscope Facility (CRFS-LMF) / Bonn

Appears in the scientific report 2023

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