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  • Authors: A Boyle;
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  • Authors: Brunson, Jessi L; Pyke, David A; Perakis, Steven S;

    Comma-separated values (.csv) files containing data related to plant biomass and seed production responses of invasive Bromus tectorum (cheatgrass) and Taeniatherum caput-medusae (medusahead) to varying sucrose treatments.

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  • Authors: Sairam Parthasarathy; Tauseef Siddiqi;
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    Spatial transcriptomics (ST) is revolutionizing tissue analysis by preserving spatial context, yet achieving spatial whole transcriptomics at single-cell resolution remains challenging. Here we present Spotiphy (Spot imager with pseudo single-cell resolution histology), a novel method and toolkit, that combines the power of generative modeling with single-cell RNA sequencing (scRNA-seq) data and high-resolution histological images to transform sequencing-based, spot-level ST data into single-cell level ST images with whole transcriptome of all detectable nuclei. In performance evaluations that used matched scRNA-seq, Visium, Xenium, CosMx, and immunohistochemistry (IHC) datasets for Alzheimer’s Disease (AD) and normal mouse brains, Spotiphy outperforms existing methods both in accuracy and short runtime. Applying Spotiphy to these datasets reveals regional specifications of astrocytes and microglia with unique expression profiles in AD mouse brains. Multiple spatial domains are identified when applying Spotiphy to ST data of human breast cancer. It further identified tumor and tumor microenvironment (TME) interaction changes across them. Spotiphy also performs cell-type proportion imputation of the non-captured area to achieve pseudo single-cell whole-slide ST images. Spotiphy overcomes the limitations of sequencing and image-based ST approaches to generate spatial whole transcriptomic profiles with single-cell resolution across the whole slide.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: Datacite
      addClaim

      This Research product is the result of merged Research products in OpenAIRE.

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  • Authors: A Boyle;
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  • Authors: A Boyle;
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852,072 Research products
  • Authors: A Boyle;
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    This Research product is the result of merged Research products in OpenAIRE.

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  • Authors: A Boyle;
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  • Authors: Brunson, Jessi L; Pyke, David A; Perakis, Steven S;

    Comma-separated values (.csv) files containing data related to plant biomass and seed production responses of invasive Bromus tectorum (cheatgrass) and Taeniatherum caput-medusae (medusahead) to varying sucrose treatments.

    addClaim

    This Research product is the result of merged Research products in OpenAIRE.

    You have already added works in your ORCID record related to the merged Research product.
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  • Authors: Sairam Parthasarathy; Tauseef Siddiqi;
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    Spatial transcriptomics (ST) is revolutionizing tissue analysis by preserving spatial context, yet achieving spatial whole transcriptomics at single-cell resolution remains challenging. Here we present Spotiphy (Spot imager with pseudo single-cell resolution histology), a novel method and toolkit, that combines the power of generative modeling with single-cell RNA sequencing (scRNA-seq) data and high-resolution histological images to transform sequencing-based, spot-level ST data into single-cell level ST images with whole transcriptome of all detectable nuclei. In performance evaluations that used matched scRNA-seq, Visium, Xenium, CosMx, and immunohistochemistry (IHC) datasets for Alzheimer’s Disease (AD) and normal mouse brains, Spotiphy outperforms existing methods both in accuracy and short runtime. Applying Spotiphy to these datasets reveals regional specifications of astrocytes and microglia with unique expression profiles in AD mouse brains. Multiple spatial domains are identified when applying Spotiphy to ST data of human breast cancer. It further identified tumor and tumor microenvironment (TME) interaction changes across them. Spotiphy also performs cell-type proportion imputation of the non-captured area to achieve pseudo single-cell whole-slide ST images. Spotiphy overcomes the limitations of sequencing and image-based ST approaches to generate spatial whole transcriptomic profiles with single-cell resolution across the whole slide.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: Datacite
    addClaim

    This Research product is the result of merged Research products in OpenAIRE.

    You have already added works in your ORCID record related to the merged Research product.
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: Datacite
      addClaim

      This Research product is the result of merged Research products in OpenAIRE.

      You have already added works in your ORCID record related to the merged Research product.
  • Authors: A Boyle;
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  • Authors: A Boyle;
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