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Single-cell RNA-sequencing of IL-21-tRFP+ GP66+ splenic CD4+ T cells on days 7 and 14 post LCMV Cl13 infection

ABSTRACT: Single-cell RNA-sequencing of IL-21-tRFP+ GP66+ splenic CD4+ T cells on days 7 and 14 post LCMV Cl13 infection

PROVIDER: PRJNA798421 | ENA |

REPOSITORIES: ENA

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Single-cell RNA-sequencing of IL-21-tRFP+ GP66+ splenic CD4+ T cells on days 7 and 14 post LCMV Cl13 infection

Project description:CD4+ T cell-derived interleukin 21 (IL-21) sustains CD8+ T cell responses during chronic viral infection, but the helper subset that confers this protection remains unclear. Here, we applied scRNA and ATAC-seq approaches to determine the heterogeneity of IL-21+CD4+ T cells during LCMV clone 13 infection.

2022-02-25 | GSE193935 | GEO

Pair-feeding of LCMV Cl13 infected mice

Project description:Mice were infected with LCMV Cl13 and food intake was measured up to 8dpi. Another group of uninfected mice received the amount of food the infected mice consumed. The third group of naïve mice received food ad libitum.

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ATAC-sequencing of Th1, Tfh, and memory-like splenic CD4+ T cells on day 14 post LCMV Cl13 infection

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Bulk RNA seq of intestinal immune cells from naïve, LCMV-Arm and LCMV-Cl13 infected mice

Project description:We report that the gastrointestinal tract (GIT) is a previously unappreciated long-term reservoir of chronic LCMV-Cl13 infection, and, chronic viral replication in the GIT has a profound effect on the local immune compartment as well as the development of subsequent immune responses. CD45+ immune cells were sorted and analyzed by RNAseq from the small and large intestines of naive mice, or mice infected 30 days prior with LCMV-Arm (acute virus) or LCMV-Cl13 (chronic virus). We show that GIT immune cells from acute and chronically infected mice differ substantially from naive mice; chronically infected mice show increases in genetic pathways involved in T cell activation and killing, inflammasome activation and interferon signaling; chronically infected mice show reduced expression of genes involved in T cell memory and antigen presenting cell activation; and chronic infection induces metabolic changes unique to the small but not large intestinal immune compartment.

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Pair-feeding of LCMV Cl13 infected mice

Project description:Pair-feeding of LCMV Cl13 infected mice

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Bulk RNA-sequencing of IL-21-tRFP+ CD44+ Th1, Tfh, and memory-like CD4+ T cell subsets on day 14 post LCMV Cl13 infection

2022-02-25 | GSE193934 | GEO

ATAC-sequencing of Th1, Tfh, and memory-like splenic CD4+ T cells on day 14 post LCMV Cl13 infection

Project description:ATAC-sequencing of Th1, Tfh, and memory-like splenic CD4+ T cells on day 14 post LCMV Cl13 infection

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RNA-seq of LCMV GP33-specific CD8 TCR transgenic cells (P14) primed at the onset versus in the midst of persistent LCMV-Clone 13 viral infection

Project description:Altered CD8 T cell differentiation and functional exhaustion prevent control of chronic virus infection and cancer. Yet, how fate commitment and exhaustion are determined and dynamically modulated throughout persistent infection are unclear. We compared the activation and differentiation of LCMV GP33-specific CD8 TCR transgenic cells (P14) primed at the onset versus in the midst of established persistent LCMV-Clone 13 viral infection. LCMV GP33-specific CD8 TCR transgenic (P14) cells were injected into naïve mice immediately infected with LCMV-Cl13 (Early priming) or into mice that had been infected 21 days earlier with LCMV-Cl13 (Late Priming). Sixty hours post-priming P14 cells were sorted from mice and subjected to RNA seq. We show early primed cells very rapidly exhibit a transcriptional profile of robust activation, effector differentiation and dysfunction, while late primed cells have increased expression of genes involved in memory differentiation and maintenance.

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Gene expression changes in liver upon LCMV Cl13 infection

Project description:Gene expression changes in liver upon LCMV Cl13 infection

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Naïve and LCMV Cl13 infected liver tissue of ERT2 AlbCre Ifnar1 fl/fl mice

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