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Genome-wide Spatial Expression Profiling in FFPE Tissues

Eva Gracia Villacampa, Ludvig Larsson, Linda Kvastad, View ORCID ProfileAlma Andersson, Joseph Carlson, View ORCID ProfileJoakim Lundeberg
doi: https://doi.org/10.1101/2020.07.24.219758
Eva Gracia Villacampa
1Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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Ludvig Larsson
1Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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Linda Kvastad
1Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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Alma Andersson
1Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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  • ORCID record for Alma Andersson
Joseph Carlson
2Department of Oncology-Pathology, Karolinska Institute, Solna, Sweden, and Department of Pathology and Cytology, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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Joakim Lundeberg
1Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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  • ORCID record for Joakim Lundeberg
  • For correspondence: joakim.lundeberg@scilifelab.se
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Abstract

Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here we present a procedure to perform genome-wide spatial analysis of mRNA in FFPE tissue sections. The procedure takes advantage of 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. First, we conducted 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. Second, we explored the spatial composition of transcriptomic signatures in ovarian carcinosarcoma samples using data driven analysis methods, exemplifying the method’s potential to elucidate molecular mechanisms in heterogeneous clinical samples.

Competing Interest Statement

JL, EVG, LL, LK, AA are scientific advisors to 10x Genomics Inc, which holds IP rights to the ST technology.

Footnotes

  • https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Adult_Mouse_Brain

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted July 25, 2020.
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Genome-wide Spatial Expression Profiling in FFPE Tissues
Eva Gracia Villacampa, Ludvig Larsson, Linda Kvastad, Alma Andersson, Joseph Carlson, Joakim Lundeberg
bioRxiv 2020.07.24.219758; doi: https://doi.org/10.1101/2020.07.24.219758
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Genome-wide Spatial Expression Profiling in FFPE Tissues
Eva Gracia Villacampa, Ludvig Larsson, Linda Kvastad, Alma Andersson, Joseph Carlson, Joakim Lundeberg
bioRxiv 2020.07.24.219758; doi: https://doi.org/10.1101/2020.07.24.219758

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