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Dynamic fibroblast-immune interactions shape recovery after brain injury [Visium]

ABSTRACT: Dynamic fibroblast-immune interactions shape recovery after brain injury [Visium]

PROVIDER: PRJNA1068655 | ENA |

REPOSITORIES: ENA

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Dynamic fibroblast-immune interactions shape recovery after brain injury [Visium]

Project description:Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used spatial transcriptomics (10X Visium) to spatiotemporally profile CNS wound healing responses, including stromal and immune responses, after photothrombotic (PT) injury.

2025-06-30 | GSE254161 | GEO

Dynamic fibroblast-immune interactions shape recovery after brain injury

Project description:Dynamic fibroblast-immune interactions shape recovery after brain injury

| PRJNA1068654 | ENA

Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Cxcl12]

Project description:Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Cxcl12]

| PRJNA1245690 | ENA

Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Tgfb]

Project description:Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Tgfb]

| PRJNA1068656 | ENA

Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Timecourse]

Project description:Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Timecourse]

| PRJNA1068657 | ENA

Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Tgfb]

Project description:Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used single nuclear RNA sequencing at multiple timepoints after photothrombotic (PT) injury to test the role of TGFb in regulating fibroblast and macrophage responses to brain injury. We find that inhibition of fibroblast TGFb signaling, or of TGFb activation, impairs profibrotic fibroblast (and macrophage) expansion and function.

2025-06-30 | GSE254163 | GEO

Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Cxcl12]

Project description:Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used single nuclear RNA sequencing at 21 days post photothrombotic (PT) injury to test the role of fibroblast-derived CXCL12 in regulating local immunity after brain injury. We find that loss of fibroblast CXCL12 causes dysregulated immune tone with elevated IFNg signaling.

2025-06-30 | GSE293682 | GEO

Dynamic fibroblast-immune interactions shape recovery after brain injury

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

2025-06-30 | GSE254164 | GEO

Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Timecourse]

Project description:Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used single nuclear RNA sequencing at multiple timepoints to profile stromal and immune responses to sterile (photothrombotic, PT) injury. We find that early pro-fibrotic myofibroblasts transition into several states, including meningeal and lymphocyte-interactive fibroblasts.

2025-06-30 | GSE254162 | GEO

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.

2024-11-01 | E-MTAB-14560 | biostudies-arrayexpress

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