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Transcriptional characterization of PD-1 positive and negative Foxp3 negative CD4 positive T cells from liver of 5- and 10-day-old Aire-deficient C57BL/6 mice

ABSTRACT: Transcriptional characterization of PD-1 positive and negative Foxp3 negative CD4 positive T cells from liver of 5- and 10-day-old Aire-deficient C57BL/6 mice

PROVIDER: PRJNA525690 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8670860_1.fastq.gz	Fastqsanger.gz
	SRR8670860_2.fastq.gz	Fastqsanger.gz
	SRR8670861_1.fastq.gz	Fastqsanger.gz
	SRR8670861_2.fastq.gz	Fastqsanger.gz
	SRR8670862_1.fastq.gz	Fastqsanger.gz

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Project description:Background. T cells in the thymus undergo opposing positive and negative selection processes so that the only T cells entering circulation are those bearing a T cell receptor (TCR) with a low affinity for self. The mechanism differentiating negative from positive selection is poorly understood, despite the fact that inherited defects in negative selection underlie organ-specific autoimmune disease in AIRE-deficient people and the non obese diabetic (NOD) mouse strain. Results. Here we use homogeneous populations of T cells undergoing either positive or negative selection in vivo together with genome-wide transcription profiling on microarrays to identify the gene expression differences underlying negative selection to an Aire-dependent organ-specific antigen, including the upregulation of a genomic cluster in the cytogenetic band 2F. Analysis of defective negative selection in the autoimmune-prone NOD strain demonstrates a global impairment in the induction of the negative selection response gene set, but little difference in positive selection response genes. Combining expression differences with genetic linkage data we identify differentially expressed candidate genes including Bim, Bnip3, Smox, Pdrg1, Id1, Pdcd1, Ly6c, Pdia3, Trim30 and Trim12. Conclusions. The data provide a molecular map of the negative selection response in vivo, and by analysis of deviations from this pathway in the autoimmune susceptible NOD strain, suggest that susceptibility arises from small expression differences in genes acting at multiple points in the pathway between the TCR and cell death. Experiment Overall Design: Analysis of two thymic populations - early single positive thymocytes (CD4+CD8lowCD69+TCRhi) and early double positive thymocytes (CD4+CD8+CD69-TCRlow). Samples purified from the 3A9 TCR transgenic (TCR) to characterise positive selection and the 3A9 TCR x insHEL double transgenic (Dbl) to characterise negative selection towards an Aire-dependent organ-specific antigen. Both the non autoimmune C57BL10.H2k (B10) and autoimmune Non obese diabetic (NOD) strains were analysed in this method. Three biological replicates were used for each of these eight different groups.

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Transcriptional characterization of PD-1 positive and negative Foxp3 negative CD4 positive T cells from liver of 5- and 10-day-old Aire-deficient C57BL/6 mice

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