Distinct T cell functions enable efficient immunoediting and prevent tumor emergence in developing sarcomas
Data files
Sep 11, 2025 version files 12.41 GB
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BH.rds
46.56 MB
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KP_RAGneg_MMT_S2_L006_I1_001.fastq.gz
319.13 MB
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KP_RAGneg_MMT_S2_L006_I2_001.fastq.gz
282.79 MB
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KP_RAGneg_MMT_S2_L006_R1_001.fastq.gz
2.21 GB
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KP_RAGneg_MMT_S2_L006_R2_001.fastq.gz
2.22 GB
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KP_RAGpos_MMT_S1_L006_I1_001.fastq.gz
268.45 MB
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KP_RAGpos_MMT_S1_L006_I2_001.fastq.gz
273.13 MB
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KP_RAGpos_MMT_S1_L006_R1_001.fastq.gz
2.19 GB
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KP_RAGpos_MMT_S1_L006_R2_001.fastq.gz
2.19 GB
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P_only_MMT_S3_L006_I1_001.fastq.gz
133.97 MB
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P_only_MMT_S3_L006_I2_001.fastq.gz
142.48 MB
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P_only_MMT_S3_L006_R1_001.fastq.gz
1.07 GB
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P_only_MMT_S3_L006_R2_001.fastq.gz
1.07 GB
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README.md
3.99 KB
Abstract
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.
Dataset DOI: 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.