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000281805 245__ $$aCode: The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.
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000281805 520__ $$aThis 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`.
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000281805 7001_ $$0P:(DE-2719)9001465$$aPérez-Jiménez, María José$$b1
000281805 7001_ $$0P:(DE-2719)9001762$$aBertoli, Federico$$b2
000281805 7001_ $$0P:(DE-2719)9001799$$aRaji, Hariam$$b3$$udzne
000281805 7001_ $$0P:(DE-2719)9001801$$aWeissleder, Christin$$b4
000281805 773__ $$a10.5281/ZENODO.17294147
000281805 7870_ $$0DZNE-2025-01192$$aPérez-Jiménez, María José et.al.$$dZenodo, 2025$$iRelatedTo$$tDataset: Supplementary Figures Tabular Data - The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.
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