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001     281805
005     20251114102930.0
024 7 _ |a 10.5281/ZENODO.17294147
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037 _ _ |a DZNE-2025-01191
100 1 _ |a Deleidi, Michela
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245 _ _ |a Code: The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.
260 _ _ |a Zenodo
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520 _ _ |a 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`.
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700 1 _ |a Pérez-Jiménez, María José
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700 1 _ |a Bertoli, Federico
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700 1 _ |a Raji, Hariam
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700 1 _ |a Weissleder, Christin
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773 _ _ |a 10.5281/ZENODO.17294147
787 0 _ |a Pérez-Jiménez, María José et.al.
|0 DZNE-2025-01192
|t Dataset: Supplementary Figures Tabular Data - The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.
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856 4 _ |u https://pub.dzne.de/record/281805/files/DZNE-2025-01191.zip
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