---
OA_place: repository
_id: '18471'
abstract:
- lang: eng
  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. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: M-Shop
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
citation:
  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>
  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>
  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>.
  ieee: N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with
    tissue context,” Institute of Science and Technology Austria, 2024.
  ista: Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape
    with tissue context. Institute of Science and Technology Austria.
  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>.
  short: N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with
    Tissue Context, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-10-26T20:02:42Z
date_published: 2024-10-28T00:00:00Z
date_updated: 2025-05-08T09:46:24Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18471
ec_funded: 1
file:
- access_level: closed
  checksum: 6d7c7725d040d8debc070dcb35ac965d
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  creator: nagudelo
  date_created: 2024-10-26T22:29:06Z
  date_updated: 2025-05-05T22:30:04Z
  embargo_to: open_access
  file_id: '18475'
  file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx
  file_size: 183077763
  relation: source_file
- access_level: open_access
  checksum: 52f9c0bf2bdafa3baf827b73814a53ff
  content_type: application/pdf
  creator: nagudelo
  date_created: 2024-10-26T23:13:33Z
  date_updated: 2025-05-05T22:30:04Z
  embargo: 2025-05-05
  file_id: '18476'
  file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf
  file_size: 47027710
  relation: main_file
file_date_updated: 2025-05-05T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '97'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
publication_identifier:
  isbn:
  - 978-3-99078-044-2
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
title: Visualizing the neuronal transcriptional landscape with tissue context
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...