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Genome-wide spatial...
Genome-wide spatial expression profiling in formalin-fixed tissues
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- Villacampa, Eva Gracia (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Larsson, Ludvig (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Mirzazadeh, Reza (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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visa fler...
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- Kvastad, Linda (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Andersson, Alma (författare)
- Karolinska Institutet,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Mollbrink, Annelie (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Kokaraki, Georgia (författare)
- Department of Oncology-Pathology, Karolinska Institute, 17176 Stockholm, Sweden
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- Monteil, Vanessa (författare)
- Karolinska Institutet
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- Schultz, Niklas (författare)
- Karolinska Institutet
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- Appelberg, Karin Sofia (författare)
- Public Health Agency of Sweden, 17182, Solna, Sweden
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- Montserrat, Nuria (författare)
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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- Zhang, Haibo (författare)
- Departments of Anesthesia, Medicine, and Physiology, University of Toronto, Keenan Research Centre for Biomedical Science, Unity Health Toronto, Toronto, ON, Canada
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- Penninger, Josef M. (författare)
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, V6T 1Z3 Vancouver, BC, Canada; Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria, Dr. Bohr-Gasse 3
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- Miesbach, Wolfgang (författare)
- Department of Haemostaseology and Haemophilia Center, Institute of Transfusion Medicine, Medical Clinic 2, University Hospital Frankfurt, 60590 Frankfurt am Main, Germany
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- Mirazimi, Ali (författare)
- Department of Laboratory Medicine, Unit of Clinical Microbiology Karolinska Institutet and Karolinska University Hospital, 17177 Stockholm, Sweden; Public Health Agency of Sweden, 17182, Solna, Sweden; National Veterinary Institute, 751 89 Uppsala, Sweden
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- Carlson, Joseph (författare)
- Department of Oncology-Pathology, Karolinska Institute, 17176 Stockholm, Sweden
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- Lundeberg, Joakim (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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(creator_code:org_t)
- Elsevier BV, 2021
- 2021
- Engelska.
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Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 1:3
- Relaterad länk:
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https://doi.org/10.1...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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http://kipublication...
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Abstract
Ämnesord
Stäng
- Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3′ end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
Nyckelord
- COVID-19
- FFPE
- genome-wide
- mouse brain
- organoids
- ovarian carcinosarcoma
- PFA
- SARS-CoV-2
- spatial transcriptomics
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Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Till lärosätets databas
- Av författaren/redakt...
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Villacampa, Eva ...
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Larsson, Ludvig
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Mirzazadeh, Reza
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Kvastad, Linda
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Andersson, Alma
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Mollbrink, Annel ...
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visa fler...
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Kokaraki, Georgi ...
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Monteil, Vanessa
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Schultz, Niklas
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Appelberg, Karin ...
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Montserrat, Nuri ...
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Zhang, Haibo
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Penninger, Josef ...
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Miesbach, Wolfga ...
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Mirazimi, Ali
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Carlson, Joseph
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Lundeberg, Joaki ...
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- MEDICIN OCH HÄLSOVETENSKAP
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och Klinisk medicin
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och Cancer och onkol ...
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- MEDICIN OCH HÄLSOVETENSKAP
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och Cell och molekyl ...
- Artiklar i publikationen
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Cell Genomics
- Av lärosätet
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Kungliga Tekniska Högskolan
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Karolinska Institutet