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Single cell TCR-seq of T cells isolated from MC38 mouse tumors

ABSTRACT: Single cell TCR-seq of T cells isolated from MC38 mouse tumors

PROVIDER: PRJEB32381 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3304810_1.fastq.gz	Fastqsanger.gz
	ERR3304810_2.fastq.gz	Fastqsanger.gz
	ERR3304807_1.fastq.gz	Fastqsanger.gz
	ERR3304807_2.fastq.gz	Fastqsanger.gz
	ERR3304808_1.fastq.gz	Fastqsanger.gz

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Single cell TCR-seq of T cells isolated from MC38 mouse tumors

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

2019-05-11 | E-MTAB-7918 | biostudies-arrayexpress

Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling and TCR sequencing.

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Single cell RNA-seq profiling of T cells isolated from MC38 mouse tumors

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Single-cell RNAseq of CD45 positive cells in MC38 tumors - Primary irradiated tumors and secondary non-irradiated tumors - Concurrent treatment with anti-PD-L1

Project description:Primary irradiated MC38 tumors and secondary MC38 non-irradiated tumors. Subcutaneous MC38 tumors in C57BL/6 mice Concurrent treatment with anti-PD-L1.

2023-10-15 | E-MTAB-13389 | biostudies-arrayexpress

Single cell RNA-seq profiling of T cells isolated from MC38 mouse tumors

Project description:Single cell RNA-seq profiling of T cells isolated from MC38 mouse tumors

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Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

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RNA-seq of parental MC38 and anti-PD-1 resistant MC38 subcutaneous tumors

Project description:MC38 tumors resistant to anti-PD-1 treatment (MC38-resistant) were generated through serial in vivo passaging, and global gene expression analysis was used to compare resistant and parental tumors. MC38 and MC38-resistant tumors exhibited widespread changes in global gene expression.

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Microarray of MC38-R tumors following intratumoral injection of IL-12 mRNA or control mRNA

Project description:We designed a novel intratumoral (IT) IL-12 mRNA therapy to promote local IL-12 tumor production whilst mitigating systemic effects. A single IT dose of mouse (m)IL-12 mRNA induced IFNγ and CD8+ T cell-dependent tumor regression in multiple syngeneic mouse models including MC38-R, and animals with a complete response demonstrated immunity to re-challenge. In order to further investigate the impact of mIL-12 mRNA on the MC38-R TME, we performed tumor transcriptomic evaluation 24h and 7 days after a single IT dose of 0.5 micrograms IL-12 or control mRNA. mRNA was isolated from snap-frozen syngeneic tumors using an RNeasy mini kit (Qiagen) and quantified on the Affymetrix mouse 430 2.0 microarray.

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10X single-cell RNASeq profiling of CD8+ T cells from wildtype MC38 tumors and paired peripheral blood

Project description:The ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential. However, tracking tumor antigen-specific CD8+ T cells in the blood is challenging due to their small number and limited reagents to track these cells. We asked whether paired single-cell RNA and T cell receptor (TCR) sequencing could be used to detect and characterize “tumor matching” (TM) CD8+ T cells in the blood of mice with MC38 tumors using the TCR as a molecular barcode. By leveraging the transcriptome, we characterized these cells, and identified candidate cell surface markers for to enrich this population. These data show that the TCR can be used to identify tumor-relevant cells for characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells.

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