TY  - JOUR
AU  - Carraro, Caterina
AU  - Bonaguro, Lorenzo
AU  - Srinivasa, Rachana
AU  - van Uelft, Martina
AU  - Isakzai, Victoria
AU  - Schulte-Schrepping, Jonas
AU  - Gambhir, Prerna
AU  - Elmzzahi, Tarek
AU  - Montgomery, Jessica V
AU  - Hayer, Hannah
AU  - Li, Yuanfang
AU  - Theis, Heidi
AU  - Kraut, Michael
AU  - Mahbubani, Krishnaa T
AU  - Aschenbrenner, Anna C
AU  - König, Ireen
AU  - Fava, Eugenio
AU  - Fried, Hans-Ulrich
AU  - De Domenico, Elena
AU  - Beyer, Marc
AU  - Saglam, Adem
AU  - Schultze, Joachim L
TI  - Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq.
JO  - Cell reports / Methods
VL  - 3
IS  - 10
SN  - 2667-2375
CY  - Cambridge, MA
PB  - Cell Press
M1  - DZNE-2023-01044
SP  - 100598
PY  - 2023
AB  - 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.
KW  - Chromatin: genetics
KW  - Chromatin Immunoprecipitation Sequencing
KW  - Laser Capture Microdissection
KW  - Gene Expression Profiling
KW  - Freezing
KW  - ATAC-seq (Other)
KW  - CP: Molecular biology (Other)
KW  - chromatin accessibility (Other)
KW  - epigenomics (Other)
KW  - laser capture microdissection (Other)
KW  - spatial omics (Other)
KW  - Chromatin (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C2  - pmc:PMC10626193
C6  - pmid:37776856
DO  - DOI:10.1016/j.crmeth.2023.100598
UR  - https://pub.dzne.de/record/265800
ER  -