# Bresesti_Cell_Reports_2025

**Reprogramming liver metastasis-associated macrophages towards an anti-tumoral phenotype through enforced miR-342 expression**

Bresesti C, Monti M, Beretta S, Merelli I, Squadrito M, _et al._; 2025

Corresponding Author: Mario Leonardo Squadrito. Email: squadrito.mario@hsr.it.  [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40Mariosqua)](https://x.com/Mariosqua)

GEO:  
[GSE274043](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274043) (single-cell RNA-seq)  
[GSE274044](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274044) (RNA-seq on iKCs)  
[GSE274045](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274045) (small RNA-seq on splenic and hepatic cell populations)  
[GSE274046](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274046) (bulk RNA-seq on splenic and hepatic cell populations)  


## Directories and Files

- environment_singlecell5.yml: contains the conda virtual environment that can be used to install all the dependencies.
- scripts: folder with R scripts used for the analyses
    - CB2025_figure_1_RNAseq.R
    - CB2025_figure_3_RNAseq.R
    - CB2025_figure_5_scRNAseq.R
    - TCGA_analysis.R
- data: results of the analyses
    - plots
    - tables
- reference
    - regev_lab_cell_cycle_mouse.rds: contains the genes involved in the cell cycle in mouse
    - miDB_sig5.MLS.rds: reference files for GSEA analysis
    - miDB_sig5.MLS_cytokines.rds: reference files for GSEA analysis

## scRNAseq analysis
The initial preprocessing of the data, including mapping against the _Mus musculus_ GRCm38 reference genome and gene counting, was done using the 10x Genomics Cell Ranger Software (v7.2.0) using default parameters. The resulting data were imported into R and analyzed with the Seurat package (v5.0.1).