DOI: 10.5061/dryad.v6wwpzh7c
title: Distinct T cell functions enable efficient immunoediting and prevent tumor emergence in developing sarcomas

description: 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+ cells
 of KPFRT CreER/Ai65 RagWT, KPFRT CreER/Ai65 Rag KO, and KWT PFRT
 CreER/Ai65 RagWT mice was performed with each sample in its own sequencing
 lane on an Illumina Novaseq, was processed with Cell Ranger 9.0.0 using
 the mm10 mouse genome indices from 10X Genomics. We then used R (v4.4.1)
 with Seurat (v5.2.1) for preprocessing and analysis. Cells with greater
 than 200 features and less than 10% mitochondrial reads were included. RNA
 data was normalized, scaled, and principal components were found. The
 functions FindNeighbors, FindClusters, and RunUMAP were then run using
 principal components 1-15 and a resolution of 0.5. The packages ggplot2
 (v3.5.2), ggpubr (v0.6.0), and dittoseq (v1.16.0) were used for
 visualizations.
description: # Distinct T cell functions enable efficient immunoediting and prevent
 tumor emergence in developing sarcomas Dataset DOI:
 [10.5061/dryad.v6wwpzh7c](10.5061/dryad.v6wwpzh7c) ## Description of the
 data and file structure 10X Genomics 5’scRNA-seq from sorted live singlet
 CD45- CD31- TER119- tdTomato+ cells of KPFRT CreER/Ai65 RagWT, KPFRT
 CreER/Ai65 Rag KO, and KWT PFRT CreER/Ai65 RagWT mice was performed with
 each sample loaded on to their own Chromium lane. Sequencing was performed
 on an Illumina Novaseq. This data captured early tumor cells, 7 days after
 lenti-Cre induction, from KP sarcomas with mClover neoantigen. Naming of
 sequencing files contains the sample identity and then the corresponding
 read (index, read1, read2). ### Files and variables #### File:
 KP_RAGneg_MMT_S2_L006_I1_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag KO mice #### File:
 KP_RAGneg_MMT_S2_L006_I2_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag KO mice #### File: BH.rds
 **Description:** Seurat object with processed scRNA data, metadata
 includes seurat clusters and sample identity. The R package required to
 view this file is "SeuratObject." #### File:
 KP_RAGpos_MMT_S1_L006_I1_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag WT mice #### File:
 KP_RAGpos_MMT_S1_L006_I2_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag WT mice #### File:
 P_only_MMT_S3_L006_I1_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KWT PFRT CreER/Ai65 RagWT mice #### File:
 P_only_MMT_S3_L006_I2_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KWT PFRT CreER/Ai65 RagWT mice #### File:
 KP_RAGneg_MMT_S2_L006_R1_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag KO mice #### File:
 KP_RAGneg_MMT_S2_L006_R2_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag KO mice #### File:
 P_only_MMT_S3_L006_R1_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KWT PFRT CreER/Ai65 RagWT mice #### File:
 KP_RAGpos_MMT_S1_L006_R1_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag WT mice #### File:
 P_only_MMT_S3_L006_R2_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KWT PFRT CreER/Ai65 RagWT mice #### File:
 KP_RAGpos_MMT_S1_L006_R2_001.fastq.gz **Description:** Sequencing data
 of 5’scRNA-seq from sorted live singlet CD45- CD31- TER119- tdTomato+
 cells of KPFRT CreER/Ai65 Rag WT mice ## Code/software Sequencing files
 were processed with Cell Ranger 9.0.0 using the mm10 mouse genome indices
 from 10X Genomics. Each sample was processed through Cell Ranger
 individually and were then merged via Seurat. We then used R (v4.4.1) with
 Seurat (v5.2.1) for preprocessing and analysis. Cells with greater than
 200 features and less than 10% mitochondrial reads were included. RNA data
 was normalized, scaled, and principal components were found. The functions
 FindNeighbors, FindClusters, and RunUMAP were then run using principal
 components 1-15 and a resolution of 0.5. The packages ggplot2 (v3.5.2),
 ggpubr (v0.6.0), and dittoseq (v1.16.0) were used for visualizations.