%0 Computer Program
%A Deleidi, Michela
%A Pérez-Jiménez, María José
%A Bertoli, Federico
%A Raji, Hariam
%A Weissleder, Christin
%T Code: The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.
%C Zenodo
%M DZNE-2025-01191
%D 2025
%X 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`.
%F PUB:(DE-HGF)33
%9 Software
%R 10.5281/ZENODO.17294147
%U https://pub.dzne.de/record/281805