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High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis [scRNA-seq and Visium]

ABSTRACT: High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis [scRNA-seq and Visium]

PROVIDER: PRJNA1017520 | ENA |

REPOSITORIES: ENA

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High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis [scRNA-seq and Visium]

Project description:Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical tissue samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial context, or high resolution in situ targeted gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. In one sample, we identify three molecularly distinct tumor subtypes, enabling us to define cell neighborhoods and biomarkers in the progression towards invasive carcinoma. In another sample, we identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. We demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity. However, it is the integration of these technologies that leads to even deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics.

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High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Spatial Visium FFPE Samples

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Comparing 10x Visium spatial transcriptomic technologies

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