{"month":"10","supervisor":[{"orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G"}],"has_accepted_license":"1","date_created":"2024-10-26T20:02:42Z","type":"dissertation","file_date_updated":"2025-05-05T22:30:04Z","day":"28","page":"97","OA_place":"repository","status":"public","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","author":[{"full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","first_name":"Nathalie"}],"date_updated":"2025-05-08T09:46:24Z","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"publisher":"Institute of Science and Technology Austria","file":[{"embargo_to":"open_access","checksum":"6d7c7725d040d8debc070dcb35ac965d","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","date_created":"2024-10-26T22:29:06Z","date_updated":"2025-05-05T22:30:04Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"18475","file_size":183077763,"creator":"nagudelo"},{"date_updated":"2025-05-05T22:30:04Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"18476","file_size":47027710,"creator":"nagudelo","date_created":"2024-10-26T23:13:33Z","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","embargo":"2025-05-05","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf"}],"language":[{"iso":"eng"}],"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232"}],"oa_version":"Published Version","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Visualizing the neuronal transcriptional landscape with tissue context","corr_author":"1","_id":"18471","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"year":"2024","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-044-2"]},"citation":{"apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria."},"doi":"10.15479/at:ista:18471","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. ","lang":"eng"}],"ec_funded":1,"date_published":"2024-10-28T00:00:00Z"}