Published August 16, 2023
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SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution
Authors/Creators
- 1. Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen N, Denmark, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
- 2. Champalimaud Centre for the Unknown, Lisbon, Portugal
- 3. Department of Surgery, Virginia Commonwealth University, School of Medicine, 1200 E Broad St. P.O. Box 980011, Richmond VA, 23298, USA
- 4. Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- 5. Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
- 6. VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA USA
Description
All data and analysis involved in the manuscript "SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution"
Files
SC2Spa_AllAnalysis.zip
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References
- Karaiskos N, Wahle P, Alles J, Boltengagen A, Ayoub S, Kipar C, Kocks C, Rajewsky N, Zinzen RP: The Drosophila embryo at single-cell transcriptome resolution. Science 2017, 358:194-199.
- Stickels RR, Murray E, Kumar P, Li J, Marshall JL, Di Bella DJ, Arlotta P, Macosko EZ, Chen F: Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nature Biotechnology 2020.
- Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, et al: Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 2016, 353:78-82.
- Chen A, Liao S, Cheng MN, Ma KL, Wu L, Lai YW, Qiu XJ, Yang J, Xu JS, Hao SJ, et al: Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 2022, 185:1777-+.
- Kleshchevnikov V, Shmatko A, Dann E, Aivazidis A, King HW, Li T, Elmentaite R, Lomakin A, Kedlian V, Gayoso A, et al: Cell2location maps fine-grained cell types in spatial transcriptomics. Nat Biotechnol 2022, 40:661-671.
- Saunders A, Macosko EZ, Wysoker A, Goldman M, Krienen FM, de Rivera H, Bien E, Baum M, Bortolin L, Wang SY, et al: Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain. Cell 2018, 174:1015-+.
- Li R, Ferdinand JR, Loudon KW, Bowyer GS, Laidlaw S, Muyas F, Mamanova L, Neves JB, Bolt L, Fasouli ES, et al: Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell 2022, 40:1583-1599 e1510.
- Janesick A, Shelansky R, Gottscho AD, Wagner F, Rouault M, Beliakoff G, Oliveira MFd, Kohlway A, Abousoud J, Morrison CA, et al: High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue. bioRxiv 2022:2022.2010.2006.510405.