TY  - COMP
AU  - Deleidi, Michela
AU  - Pérez-Jiménez, María José
AU  - Bertoli, Federico
AU  - Raji, Hariam
AU  - Weissleder, Christin
TI  - Code: The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.
CY  - Zenodo
M1  - DZNE-2025-01191
PY  - 2025
AB  - 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`.
LB  - PUB:(DE-HGF)33
DO  - DOI:10.5281/ZENODO.17294147
UR  - https://pub.dzne.de/record/281805
ER  -