Software

DZNE-2025-01191

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Code: The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.

Deleidi, M.DZNE* ; Pérez-Jiménez, M. J.Extern* ; Bertoli, F.DZNE* ; Raji, H.Extern* ; Weissleder, C.DZNE*

2025
Zenodo

This record in other databases:

Please use a persistent id in citations: doi:10.5281/ZENODO.17294147

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`.

---

Contributing Institute(s):

1. Mitochondria and Inflammation in Neurodegenerative Diseases (AG Deleidi)

Research Program(s):

1. 352 - Disease Mechanisms (POF4-352) (POF4-352)

Appears in the scientific report 2025

---

---

Linked articles:

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Dataset Pérez-Jiménez, M. J.Extern* ; Bertoli, F.DZNE* ; Weissleder, C.DZNE* ; Raji, H.Extern* ; Deleidi, M.DZNE*
Dataset: Supplementary Figures Tabular Data - The mitochondrial unfolded protein response disrupts neuronal-glial communication and promotes senescence in human microglia.
Zenodo (2025) [10.5281/zenodo.17294799]2025 BibTeX | EndNote: XML, Text | RIS

---