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I updated the scripts
Marco Monti authored
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Name Last commit Last update
reference I added the manuscript's scripts
CB2025_figure_1_RNAseq.R I updated the scripts
CB2025_figure_3_RNAseq.R I updated the scripts
CB2025_figure_5_scRNAseq.R I updated the scripts
README.md I added the manuscript's scripts
TCGA_analysis.R I updated the scripts
environment_singlecell5.yml I added the manuscript's scripts
README.md

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

GEO:
GSE274043 (single-cell RNA-seq)
GSE274044 (RNA-seq on iKCs)
GSE274045 (small RNA-seq on splenic and hepatic cell populations)
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).

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