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TRAF3 regulates TFH cell differentiation during infections (ATAC-Seq)

ABSTRACT: TRAF3 regulates TFH cell differentiation during infections (ATAC-Seq)

PROVIDER: PRJNA1008103 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25735564_1.fastq.gz	Fastqsanger.gz
	SRR25735564_2.fastq.gz	Fastqsanger.gz
	SRR25735565_1.fastq.gz	Fastqsanger.gz
	SRR25735565_2.fastq.gz	Fastqsanger.gz
	SRR25735566_1.fastq.gz	Fastqsanger.gz

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TRAF3 regulates TFH cell differentiation during infections (RNA-Seq)

Project description:Comparison of transcriptome between WT and tamoxifen-inducible deletion of TRAF3 (iTraf3−/−) SMARTA or PbTII TFH cells during the infections by LCMV armstrong and Plasmodium yoelii, respectively.

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TRAF3 regulates TFH cell differentiation during infections

Project description:TRAF3 regulates TFH cell differentiation during infections

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TRAF3 regulates TFH cell differentiation during infections (ATAC-Seq)

Project description:Comparison of chromatin accessibility between WT and tamoxifen-inducible deletion of TRAF3 (iTraf3−/−) SMARTA TFH cells during LCMV armstrong infection

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TRAF3 regulates TFH cell differentiation during infections (RNA-Seq)

Project description:TRAF3 regulates TFH cell differentiation during infections (RNA-Seq)

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TRAF3 regulates TFH cell differentiation during infections

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-02-15 | GSE241414 | GEO

TCF1 is required for the differentiation of T follicular helper (TFH) cells during viral infections

Project description:TFH and Th1 cells generated after viral or intracellular bacterial infections are critical for the control of infections and the development of immunological memories. However, the mechanisms that govern the choice of activated CD4 T cells to the two alternative fates remain unclear. Here, we found that reciprocal expression of TCF1 and Blimp1 between viral-specific TFH and Th1 cells started early after infection. TCF1 was intrinsically required for the differentiation of TFH cells. In the absence of TCF1, TFH cells failed to maintain their transcriptional and metabolic signatures, distinct from those in Th1 cells. Mechanistically, TCF1 functioned through forming negative feedback loops with IL-2 and Blimp1 signaling. Thus, we have demonstrated an essential role of TCF1 in TFH-cell differentiation. Tcf7 deficient and WT SMARTA CD4 T cells were isolated from mice 8 days after Lymphocytic Choriomeningitis Virus (LCMV) infection. TFH and Th1 cells were separated by FACS.

2015-09-18 | E-GEOD-65660 | biostudies-arrayexpress

TCF1 is required for the differentiation of T follicular helper (TFH) cells during viral infections

2015-09-18 | GSE65660 | GEO

ATAC-seq of primary human T Follicular Helper (TFH) cells and naive CD4-positive helper T cells from tonsils of healthy volunteers

Project description:Genome Wide Association Studies (GWAS) have been successful in yielding >60 loci for Systemic Lupus Erythematosus (SLE). However, it is known that GWAS just reports genomic signals and not necessarily the precise localization of culprit genes, with eQTL efforts only able to infer causality to a minority of such loci. Thus, we sought to carry out physical and direct ‘variant to gene mapping’ by integrating results from high-throughput chromatin conformation capture and ATAC-seq assays. This experiment refers to the ATAC-seq part of our work. To determine informative proxy SNPs for each of the SLE GWAS sentinel loci, we generated ATAC-seq open chromatin maps for primary human T Follicular Helper (TFH) cells from tonsils of healthy volunteers (3 biological replicates), a model relevant to SLE as TFH operate upstream of the activation of pathogenic autoantibody-producing B cells during the disease. We also generated open chromatin maps for naive CD4-positive helper T cells (3 biological replicates).

2020-05-12 | E-MTAB-6617 | biostudies-arrayexpress

RNA sequencing of NT control cells, Traf3 KO, and Traf3/p100 double KO cells

Project description:Loss of Traf3 caused a dramatic induction of innate immune response genes. Antigen presentation, interferon response genes and genes responsible for foreign DNA and RNA recognition were strongly upregulated by deletion of Traf3, but KO of p100 in Traf3 KO samples reversed the activation of these pathways. We did not detect any stimulation by Traf3 KO of those signaling pathways classically involved in proliferation, including PI3K/AKT, JNK, TGF-beta, WNT and Hippo

2020-03-31 | GSE147767 | GEO

Activin A regulates human T follicular helper (Tfh) cell differentiation

Project description:To determine the role of the cytokine activin A in the regulation of human T follicular helper (Tfh) cell gene program, we performed a transcriptomic analysis (RNA-seq) of human naÃ¯ve CD4 T cells differentiated in vitro with activin A. The analysis of the gene expression profile driven by activin A, alone or in combination with IL-12 (a know regulator of human Tfh differentiation/function), revealed that activin A can regulate the expression of multiple molecules involved in the differentiation and/or function of human Tfh cells. Human naÃ¯ve CD4 T cells were isolated from fresh PBMCs of healthy control subjects by magnetic bead isolation. Purity was measured by FACS as percentage of CD4+CD45RA+ cells and was 95% or higher. Upon isolation, naÃ¯ve CD4 T cells were stimulated with anti-CD3/CD28 coated beads in the presence of the following cytokine combinations: no exogenous cytokines (beads only), activin A, IL-12, activin A+IL-12, TGFb, TGFb +IL12. Following 5 days of in vitro culture, live CD4 T cells were FACS sorted and gene expression was analyzed by RNA-seq. Data are from independent donors.

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