I updated the README.md file

README.md

@@ -2,13 +2,16 @@
 
 **_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
+[Marco Notaro](https://orcid.org/0000-0003-4328-4835), [Marco Monti](https://orcid.org/0000-0003-1266-4325), [Stefano Beretta](https://orcid.org/0000-0003-4375-004X), [Ivan Merelli](https://orcid.org/0000-0003-3587-3680), [Mario Leonardo Squadrito](https://orcid.org/0000-0002-1188-0299), *et al.*; Nature Communications, 2025 <https://doi.org/10.1038/s41467-025-58369-2>
 
 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: [GSE273615](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE273615)
+Raw data:
+GEO: [GSE273615](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE273615)   
 ENA: [PRJEB78386](https://www.ebi.ac.uk/ena/browser/view/PRJEB78386)
 
+Additional source data required to reproduce the UMAPs is available on Open Research Data Repository (ORDR):  
+[DOI: 10.17632/3nr54vyvtk.1](https://data.mendeley.com/datasets//3nr54vyvtk/1)
 
 ## Directories and Files
 

TAD012/002_TAD012_Liver_Tetramer_and_CD4_GSEA_DOTPLOT.R

@@ -145,7 +145,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 TandNK_df <- FetchData(obs1, vars = var_list)
 TandNK_df$cell_ID <- rownames(TandNK_df)
 write.xlsx(TandNK_df, file=paste0(pdir, "/TAD12_TandNK_umap_FigS7I_S7J_S7K.xlsx"), overwrite=T)
-
+write.csv(TandNK_df, paste0(pdir, "/TAD12_TandNK_umap_FigS7I_S7J_S7K.csv"))
 
 #############Dotplot stellare############
 #load function

TAD018/001_TAD018_liver_tumor_APCs_MLS_dotplot_stellari_radarplot.R

@@ -77,6 +77,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 apcs.liver_df <- FetchData(apcs.liver, vars = var_list)
 apcs.liver_df$cell_ID <- rownames(apcs.liver_df)
 write.xlsx(apcs.liver_df, file=paste0(pdir, "/Liver_umapAPC_Fig2C.xlsx"), overwrite=T)
+write.csv(apcs.liver_df, paste0(pdir, "/Liver_umapAPC_Fig2C.csv"))
 
 pdf(paste0(pdir, "/Tumor_umapAPC_Fig2D.pdf"), width = 8, height = 6)
 DimPlot(apcs.tumor, reduction = "umap.harmony.orig.ident", group.by = "NewlablesM_clu", label = T, label.size = 6, repel = T)
@@ -86,6 +87,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 apcs.tumor_df <- FetchData(apcs.tumor, vars = var_list)
 apcs.tumor_df$cell_ID <- rownames(apcs.tumor_df)
 write.xlsx(apcs.tumor_df, file=paste0(pdir, "/Tumor_umapAPC_Fig2D.xlsx"), overwrite=T)
+write.csv(apcs.tumor_df, paste0(pdir, "/Tumor_umapAPC_Fig2D.csv"))
 
 # All Liver
 ALL_liver <- readRDS("/beegfs/scratch/ric.squadrito/ric.squadrito/90-935462466_scRNAseq_NotaroTAD_A018/Analysis_MM/results2/Liver/Liver_final.rds")
@@ -106,6 +108,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 ALL_liver_df <- FetchData(ALL_liver, vars = var_list)
 ALL_liver_df$cell_ID <- rownames(ALL_liver_df)
 write.xlsx(ALL_liver_df, file=paste0(pdir, "/Liver_umap_Fig2A_FigS4B.xlsx"), overwrite=T)
+write.csv(ALL_liver_df, paste0(pdir, "/Liver_umap_Fig2A_FigS4B.csv"))
 
 # All Tumor
 ALL_tumor <- readRDS("/beegfs/scratch/ric.squadrito/ric.squadrito/90-935462466_scRNAseq_NotaroTAD_A018/Analysis_MM/results2/Tumor/Tumor_final.rds")
@@ -126,6 +129,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 ALL_tumor_df <- FetchData(ALL_tumor, vars = var_list)
 ALL_tumor_df$cell_ID <- rownames(ALL_tumor_df)
 write.xlsx(ALL_tumor_df, file=paste0(pdir, "/Tumor_umap_Fig2B_FigS4C.xlsx"), overwrite=T)
+write.csv(ALL_tumor_df, paste0(pdir, "/Tumor_umap_Fig2B_FigS4C.csv"))
 
 # Macrophages Tumor
 macrophages_tumor <- readRDS("/beegfs/scratch/ric.squadrito/ric.squadrito/90-935462466_scRNAseq_NotaroTAD_A018/Analysis_MM/results3/macrophages_tumor/macrophages_tumor_final.rds")
@@ -146,6 +150,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 macrophages_tumor_df <- FetchData(macrophages_tumor, vars = var_list)
 macrophages_tumor_df$cell_ID <- rownames(macrophages_tumor_df)
 write.xlsx(macrophages_tumor_df, file=paste0(pdir, "/macrophages_tumor_umap_res.0.3_FigS5C.xlsx"), overwrite=T)
+write.csv(macrophages_tumor_df, paste0(pdir, "/macrophages_tumor_umap_res.0.3_FigS5C.csv"))
 
 ##############DOTPLOT STELLARI#####################################
 # Selected genes for dotplot
@@ -200,7 +205,7 @@ a<-ggplot(df2, aes(x=features.plot, y=id, size=pct.exp ,color=avg.exp.scaled)) +
   theme(axis.line.x=element_line(color="Black"))+
   theme(axis.line.y=element_line(color="Black"))+
   ggtitle("Dotplot liver APCs")
-ggsave(filename = paste0(pdir, "/Dotplot_stellare_liverAPCs_Fig2E.pdf"), plot=1, width=11, height=3)
+ggsave(filename = paste0(pdir, "/Dotplot_stellare_liverAPCs_Fig2E.pdf"), plot=a, width=11, height=3)
 
 #############TUMOR#################################
 #####################Figure 2F####################
@@ -248,7 +253,7 @@ a<-ggplot(df2, aes(x=features.plot, y=id, size=pct.exp ,color=avg.exp.scaled)) +
   theme(axis.line.x=element_line(color="Black"))+
   theme(axis.line.y=element_line(color="Black"))+
   ggtitle("Dotplot tumor APCs")
-ggsave(filename = paste0(pdir, "/Dotplot_stellare_tumorAPCs_Fig2F.pdf"), plot=1, width=11, height=3)
+ggsave(filename = paste0(pdir, "/Dotplot_stellare_tumorAPCs_Fig2F.pdf"), plot=a, width=11, height=3)
 
 ###############RADAR PLOT WITH MACROCLASS LIVER AND TUMOR#################################
 ###############Figure 2G#################################################################

TAD018/002_TAD018_Liver_Tumor_TNK_dotplot_radar_GSEA.R

@@ -235,6 +235,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 TandNK_df <- FetchData(obs1, vars = var_list)
 TandNK_df$cell_ID <- rownames(TandNK_df)
 write.xlsx(TandNK_df, file=paste0(pdir, "/TandNK_umap_Fig3A_3E_3I.xlsx"), overwrite=T)
+write.csv(TandNK_df, paste0(pdir, "/TandNK_umap_Fig3A_3E_3I.csv"))
 
 #######################Plot UMAP################
 

TAD019/001_TAD019_APCs_analysis.R

@@ -311,11 +311,12 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 liver.apcs_df <- FetchData(liver.apcs, vars = var_list)
 liver.apcs_df$cell_ID <- rownames(liver.apcs_df)
 write.xlsx(liver.apcs_df, file=paste0(pdir, "/liver_apcs_umap_FigS11A-1.xlsx"), overwrite=T)
+write.csv(liver.apcs_df, paste0(pdir, "/liver_apcs_umap_FigS11A-1.csv"))
 
 tumor.apcs_df <- FetchData(tumor.apcs, vars = var_list)
 tumor.apcs_df$cell_ID <- rownames(tumor.apcs_df)
 write.xlsx(tumor.apcs_df, file=paste0(pdir, "/tumor_apcs_umap_FigS11A-2.xlsx"), overwrite=T)
-
+write.csv(tumor.apcs_df, paste0(pdir, "/tumor_apcs_umap_FigS11A-2.csv"))
 
 
 #################################ENDS here##############################
\ No newline at end of file

TAD019/002_TAD019_TandNK_analysis.R

@@ -230,6 +230,7 @@ var_list <- c("UMAPh_1", "UMAPh_2","Tissue","orig.ident","Sample","RNA_Group","T
 TandNK_df <- FetchData(obs1, vars = var_list)
 TandNK_df$cell_ID <- rownames(TandNK_df)
 write.xlsx(TandNK_df, file=paste0(pdir, "/AKTPF_TandNK_umap_Fig6B_FigS12F.xlsx"), overwrite=T)
+write.csv(TandNK_df, paste0(pdir, "/AKTPF_TandNK_umap_Fig6B_FigS12F.csv"))
 
 #######################Plot UMAP################