Spatial Transcriptomics correlated Electron Microscopy (MERFISH and scRNA-Seq)

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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 ...

Demyelinating injuries in the central nervous system trigger a regenerative process that relies on coordinated responses from multiple cell types, including the innate immune system. Here, we propose that a maladaptive chronic immune response may be initiated when microglia’s capacity to clear myelin debris is overwhelmed, leading to a self-propagating immune response that impairs remyelination and causes further tissue damage. We aim to identify the molecular checkpoints in microglia/macrophages ...

Understanding the complexity of cellular function within a tissue necessitates the combination of multiple phenotypic readouts. Here, we developed a method that links spatially-resolved gene expression of single cells with their ultrastructural morphology by integrating multiplexed error-robust fluorescence in situ hybridization (MERFISH) and large area volume electron microscopy (EM) on adjacent tissue sections. Using this method, we characterized in situ ultrastructural and transcriptional ...