Additional file 1 of Decoding the transcriptional heterogeneity, differentiation lineage, clinical significance in tissue-resident memory CD8 T cell of the small intestine by single-cell analysis
Creators: name: Fang, Jialing
name: Lei, Jun
name: He, Boxiao
name: Wu, Yankang
name: Chen, Peng
name: Sun, Zaiqiao
name: Wu, Ning
name: Huang, Yafei
name: Wei, Pengcheng
name: Yin, Lei
name: Chen, Yongshun
Publisher: name: figshare
Year: 2024
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1: Figure S1. Preprocessing of the scRNA-seq dataset. A Box plots indicating the gene count, UMI count, and mitochondrial gene percent in each donor. B Box plots indicating the gene count, UMI count, and mitochondrial gene percent in each T cell subset. C Box plots indicating the gene count, UMI count, and mitochondrial gene percent in each organ. D Point plot indicating the dispersions and mean expression of highly variable genes. E The box plot indicates genes with the highest fraction of counts in each single cell. F UMAP plot showing single cells collected from the CellTypist database, labeled by organs (left), library construction methods (middle), and donors (right). Figure S2. The distribution of T cell subsets in distinct organs. A Bar plots indicating the overall barcode count of distinct donors (left) and organs (middle) and the proportion of each cell subsets among organs (right). B Box plots indicating the proportion of T cell subsets in distinct organs. C Heatmaps indicating the clustering of T cell subsets based on their distribution in distinct organs. Figure S3. The transcriptomic feature of distinct organs and T cell subsets. A The dot plot indicates the expression of several marker genes in distinct organs. B The point plot indicating differential genes of T cell subsets. Genes with log2Foldchange greater than 2 and p value adjust less than 0.001 were annotated as differential genes. C Heatmaps of the overlapping of differential genes among T cell subsets. Cells with a proportion of differential genes greater than 0.7 are labeled as “ +  +  + ”. Cells with a proportion of differential genes greater than 0.5 are labeled as “ +  + ”. Cells with a proportion of differential genes greater than 0.3 are labeled as “ + ”. D The point plot indicating differential genes of the Trm_gut_CD8. Genes with abs(log2Foldchange) greater than 2 and p value adjust less than 0.001 were annotated as differential genes. E The bar plot indicating enriched pathways of Trm_gut_CD8. Figure S4. The transcriptomic feature of the Trm_gut_CD8 subset. A The dot plot indicates the top5 differential genes of the Trm_gut_CD8 among distinct intestine organs. B Heatmaps of the overlapping of differential genes Trm_gut_CD8 among distinct intestine organs. C The bar plot indicating enriched pathways of PPI gene modules of Trm_gut_CD8 among distinct intestine organs. Figure S5. The receptor &amp; ligand analysis of cell subsets in the DUO organ. A Circle plots indicating interaction numbers among cell subsets in the DUO. B Circle plots indicating interaction strength among cell subsets in the DUO. C Circle plots of the CD48 signaling pathway network and specific receptor &amp; ligand pairing among cell subsets. D Circle plots of the TNF signaling pathway network and specific receptor &amp; ligand pairing among cell subsets. E Circle plots of the LCK signaling pathway network and specific receptor &amp; ligand pairing among cell subsets. F Left, circle plots of the MHC-I signaling pathway network among cell subsets. Right, the bar plot indicates the contribution of distinct receptor &amp; ligand pairing patterns. Contribution greater than 0.01 was labeled as “detected”. Figure S6. The WGCNA analysis of the Trm_gut_CD8 from distinct intestine organs. A The summary figure of the soft-power threshold selection. B The corrplot indicating the correlation between each gene module based on their hMEs, MEs, or hub gene scores. C Top 25 hub genes in each module ranked by kME using the PlotKMEs function. D Bar plots indicating the gene ontology analyses and KEGG analyses of hub genes of each gene module. Figure S7. T cell subsets lineage tracking and the clonotypes comparison of distinct T cell subsets. A Box plots indicating index including STARTRAC-expa, STARTRAC-migr, STARTRAC-tran, STARTRAC-gini in distinct T cell subsets. B Bar plots indicating the clonotype expansion degree of T cell subsets in four intestine organs. C Heatmaps indicating the overlapping of clonotypes of distinct T cell subsets within specific organs. D Heatmaps indicating the overlapping of clonotypes of Trm_gut_CD8 among distinct organs. E Heatmaps indicating the overlapping of clonotypes of distinct T cell subsets among distinct organs. Figure S8. The distribution and transcriptomic feature of the Trm_gut_CD8 in paired tumor and normal samples. A tSNE plots indicating the T cell subsets in the query dataset split by tumor and normal samples. B Violin plots indicating predicted percent of Trm_gut_CD8 derived from distinct organs between normal and tumor tissues. C Dot plots indicating the expression levels of marker genes in Trm_gut_CD8 derived from distinct organs between normal and tumor tissues. Figure S9. The infiltration of Trm_gut_CD8 cells in the colorectal cancer benefits the overall survival and the response to the immune checkpoint blockade therapy. A Scatter plots indicating differential genes of TCGA colorectal samples with high infiltration of Trm_gut_CD8 cells in distinct organs. B The bar plot indicating the enriched signaling pathways of up-regulated genes in the panel A. C Overall survival curves of colorectal cancer patients stratified by