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Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (GeoMx)

ABSTRACT: Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (GeoMx)

PROVIDER: PRJEB81792 | ENA |

REPOSITORIES: ENA

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Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (GeoMx)

Project description:We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.

2024-11-01 | E-MTAB-14566 | biostudies-arrayexpress

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (Chromium and Visium)

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Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (Chromium and Visium)

Project description:Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (Chromium and Visium)

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Project description:In this study, we analyzed the differential spatial transcriptome of Triple-Negative Breast Cancer (TNBC) patients who responded in an opposite manner to neoadjuvant chemotherapy (NACT): we compared responders displaying pathological complete response (pCR) with no-responders who showed disease progression during therapy. Diagnostic TruCut biopsies were analyzed using the GeoMx Cancer Transcriptome Atlas (Nanostring).

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Spatial Visium FFPE Samples

Project description:Spatial Visium FFPE Samples

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Spatial localization with Spatial Transcriptomics for an atlas of healthy and injured cell states and niches in the human kidney [Visium ST]

Project description:To spatially localize cell types within the tissue, snCv3 subclasses were used to predict the corresponding identities in Visium transcriptomic data. This allowed for recapitulated renal corpuscle, tubular, vascular, and interstitial cell types having proportions, marker profiles, and spatial organizations consistent observed histopathology.

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