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@MISC{Deleidi:281805,
      author       = {Deleidi, Michela and Pérez-Jiménez, María José and
                      Bertoli, Federico and Raji, Hariam and Weissleder, Christin},
      title        = {{C}ode: {T}he mitochondrial unfolded protein response
                      disrupts neuronal-glial communication and promotes
                      senescence in human microglia.},
      address      = {Zenodo},
      reportid     = {DZNE-2025-01191},
      year         = {2025},
      abstract     = {This repository contains the R script used for the analysis
                      of single-cell RNA-sequencing (scRNA-seq) data to compare
                      two experimental conditions: a control (CTRL) and CDDO-Me
                      treatment (C3).The analysis pipeline performs the following
                      steps:* **Data Loading and Pre-processing:** Loads 10x
                      Genomics filtered feature-barcode matrices.* **Doublet
                      Detection and Removal:** Identifies and filters out
                      potential doublets using the `DoubletFinder` package.*
                      **Quality Control (QC):** Filters cells based on nUMI,
                      nGene, log10GenesPerUMI, and mitochondrial DNA ratio.*
                      **Data Integration:** Merges the two conditions and corrects
                      for batch effects using `Harmony`. Cell cycle effects and
                      mitochondrial ratio are regressed out during scaling with
                      `SCTransform`.* **Clustering and Visualization:** Performs
                      dimensionality reduction (PCA and UMAP) and identifies cell
                      clusters.* **Cell Type Annotation:** Includes code for
                      renaming clusters based on marker gene expression.*
                      **Differential Expression (DE) Analysis:** Identifies DE
                      genes between conditions within specific cell clusters using
                      `MAST`.* **Cell Signature Scoring:** Calculates gene
                      signature scores using `UCell`.* **Cell-Cell Communication
                      Analysis:** Infers and compares intercellular communication
                      networks between the two conditions using `CellChat`.},
      cin          = {AG Deleidi},
      cid          = {I:(DE-2719)1210011},
      pnm          = {352 - Disease Mechanisms (POF4-352)},
      pid          = {G:(DE-HGF)POF4-352},
      typ          = {PUB:(DE-HGF)33},
      doi          = {10.5281/ZENODO.17294147},
      url          = {https://pub.dzne.de/record/281805},
}