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A pairwise cytokine code explains the organism-wide response to sepsis [spatial transcriptomics by Visium]

ABSTRACT: A pairwise cytokine code explains the organism-wide response to sepsis [spatial transcriptomics by Visium]

PROVIDER: PRJNA929973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23290066_1.fastq.gz	Fastqsanger.gz
	SRR23290066_2.fastq.gz	Fastqsanger.gz
	SRR23290067_1.fastq.gz	Fastqsanger.gz
	SRR23290067_2.fastq.gz	Fastqsanger.gz
	SRR23290068_1.fastq.gz	Fastqsanger.gz

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A pairwise cytokine code explains the organism-wide response to sepsis

Project description:A pairwise cytokine code explains the organism-wide response to sepsis

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A pairwise cytokine code explains the organism-wide response to sepsis [Whole-tissue RNA-seq]

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A pairwise cytokine code explains the organism-wide response to sepsis [spatial transcriptomics by Visium]

Project description:Sepsis is a systemic response to infection with life-threatening consequences. Our understanding of the molecular and cellular impact of sepsis across organs remains rudimentary. Here, we characterize the pathogenesis of sepsis by measuring dynamic changes in gene expression across organs. To pinpoint molecules controlling organ states in sepsis, we compare the effects of sepsis on organ gene expression to those of 6 singles and 15 pairs of recombinant cytokines. Strikingly, we find that the pairwise effects of tumor necrosis factor plus interleukin (IL)-18, interferon-gamma or IL-1 suffice to mirror the impact of sepsis across tissues. Mechanistically, we map the cellular effects of sepsis and cytokines by computing changes in the abundance of 195 cell types across 9 organs, which we validate by whole-mouse spatial profiling. Our work decodes the cytokine cacophony in sepsis into a pairwise cytokine message capturing the gene, cell and tissue responses of the host to the disease.

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A pairwise cytokine code explains the organism-wide response to sepsis [Spatial transcriptomics by Array-seq]

Project description:A pairwise cytokine code explains the organism-wide response to sepsis [Spatial transcriptomics by Array-seq]

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A pairwise cytokine code explains the organism-wide response to sepsis [Whole-tissue RNA-seq]

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2024-01-08 | GSE248904 | GEO

A pairwise cytokine code explains the organism-wide response to sepsis

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

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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: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.

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