Notaro_Mouse_LM_2025
In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation
Notaro M, Monti M, Beretta S, Merelli I, Squadrito M, et al.; 2025
Corresponding Author: Mario Leonardo Squadrito. Email: squadrito.mario@hsr.it. 
GEO: GSE273615 ENA: PRJEB78386
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
- TAD012
- 001_TAD012_APCs_analysis_liver.R
- 002_TAD012_Liver_Tetramer_and_CD4_GSEA_DOTPLOT.R
- TAD018
- 000_TAD018_liver_tumor_dot_plot_markers.R
- 001_TAD018_liver_tumor_APCs_MLS_dotplot_stellari_radarplot.R
- 002_TAD018_Liver_Tumor_TNK_dotplot_radar_GSEA.R
- 003_TAD018_Alluvial_plot.R
- TAD019
- 001_TAD019_APCs_analysis.R
- 002_TAD019_TandNK_analysis.R
- 003_TAD019_Multinichenet_Tumor.R
- Vizgen
- Vizgen_transcript_distance_heatmap.R
- Vizgen_transcript_distance.R
- antigen_discovery
- 001_antigen_discovery_filtering.R
- 002_antigen_discovery_VCF_double_mutations.R
- Others
- plot_stellare_function.R
- TAD012
- 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_sig4.MLS.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).