Expression profiling: MERFISH Spatial Transcriptomics (mouse)

https://rdp.sfb274.de/ (Research Data Platform) https://gepris.dfg.de/gepris/projekt/408885537 (DFG Gepris entry) The central nervous system (CNS) is a terminally differentiated tissue, where any insult carries a heightened risk - yet the tissue response to these insults is variable and can range from irreversible destruction to almost complete recovery. The rules that instruct these divergent outcomes are still unknown. The aim of this CRC is therefore to understand the biology of the multicellular ...

The cerebral cortex contains a special, perineuronally localized population of oligodendrocyte lineage cells with possible functions in connectivity and myelination. We hypothesize that this cell population serves as a reservoir of remyelinating cells after myelin damage. We will apply spatial transcriptome analysis with subcellular resolution in experimental models of demyelination and human tissue from patients with multiple sclerosis to define physiological and pathological states of perineuronal ...

Compartmentalized inflammation is a key driver of multiple sclerosis (MS) progression, but the mechanisms sustaining its persistence remain unclear. A hallmark of this persistent and slowly evolving inflammatory process is chronic active MS lesions. We generated a high-resolution, single-cell molecular and spatial atlas of such lesions by combining single-nucleus RNA sequencing (snRNA-seq) with multiplexed error-robust fluorescence in situ hybridization (MERFISH). Within lesion rims, we identified ...

Primary mouse microglia were purified from early postnatal brains, seeded on coated slides in defined medium, and exposed to a myelin plus IFN-γ activation regimen. After fixation and permeabilization, a 500-gene MERFISH panel was applied to spatially resolve lipid-metabolism and inflammatory transcripts at single-cell resolution, enabling unbiased identification of distinct microglial states across the culture.