Extended Data Fig. 5: Quality control for single-cell sequencing analysis on tumor-reactive TILs. | Nature Cancer

Extended Data Fig. 5: Quality control for single-cell sequencing analysis on tumor-reactive TILs.

From: Impaired T cell and neoantigen retention in time-serial analysis of metastatic non-small cell lung cancer in patients unresponsive to TIL cell therapy

Extended Data Fig. 5

a, Batch effect quality control of single-cell RNA sequencing of TIL for each patient. nFeature_RNA: the number of genes; nCount_RNA: the number of reads; percent.mt: percentage of reads mapped to mitochondrial genes. b, A UMAP plot showing analyzed TIL cells colored by patients. c, Metrics to evaluate single-cell sequencing data integration quality. LISI, Local Inverse Simpson’s Index; iLISI, integration LISI; cLISI, cell type LISI; CiLISI, cell type integration LISI; ASW, Average Sihouette Width. d, Marker plots and QC for major cell types. e, UMAP projections of 52,830 T cells from 8 total TIL samples. f-g, Nonscaled gene expression UMAP for each marker was shown in CD4+TIL (f) and CD8+TIL (g), with their corresponding cell annotation UMAPs presented on the top left in each panel. Abbreviations: Tm: memory T; Tcytotoxic: cytotoxic T; Tstemlike: stem-like T; Teff: effector T; Tem: effector memory T; Tex: exhausted T; Tprolif: proliferating T; Tfh: follicular helper T; Treg: regulatory T.

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