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ATAC-seq analysis of murine thymic iNKT subsets from C57BL/6 mice and Hivep3-deficient mice

ABSTRACT: ATAC-seq analysis of murine thymic iNKT subsets from C57BL/6 mice and Hivep3-deficient mice

PROVIDER: PRJNA673423 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12953111_1.fastq.gz	Fastqsanger.gz
	SRR12953111_2.fastq.gz	Fastqsanger.gz
	SRR12953112_1.fastq.gz	Fastqsanger.gz
	SRR12953112_2.fastq.gz	Fastqsanger.gz
	SRR12953113_1.fastq.gz	Fastqsanger.gz

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ATAC-seq analysis of murine thymic iNKT subsets from C57BL/6 mice and Hivep3-deficient mice

Project description:ATAC-seq analysis of murine thymic iNKT subsets from two independent C57BL/6 mice and two independent Hivep3-deficient mice

2020-10-31 | GSE160518 | GEO

Single-cell RNA transcriptomics of thymic iNKT cells from C57BL/6 and Hivep3-/- mice

Project description:Single-cell RNA-seq analysis of murine thymic iNKT cells from two independent C57BL/6 mice and two independent Hivep3-deficient mice

2020-11-06 | GSE152786 | GEO

TCR signal strength controls thymic differentiation of iNKT cell subsets

Project description:TCR signal strength controls thymic differentiation of iNKT cell subsets

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TCR signal strength controls thymic differentiation of iNKT cell subsets

Project description:TCR signal strength controls thymic differentiation of iNKT cell subsets

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The Effect of PRMT5 deficiency on thymic iNKT cells

Project description:Protein arginine methylation is a post-translational modification catalyzed by protein arginine methyltransferase (PRMT). To elucidate the role of PRMT5 in T cells, we generated T-cell specific PRMT5-deficient mice (Prmt5 flox/d Cd4-Cre mice) and found a severe loss of thymic iNKT cells as well as a reduced number in peripheral CD4+ and CD8+ T cells. As iNKT cells were significantly decreased in the stage 1, 2 and 3 of developmental stages, RNA-seq was performed using stage 1 iNKT cells of control and PRMT5-deficient mice. This transcriptome analysis will provide mechanistic insight into how PRMT5 contributes to thymic iNKT cell development.

2018-08-06 | GSE118135 | GEO

Single-cell RNA transcriptomics of thymic iNKT cells from BALB/c and Cd80/Cd86 -/- (B7KO) mice

Project description:Single-cell RNA-seq analysis of murine thymic iNKT cells from three independent BALB/c mice and three independent Cd80/Cd86 (B7)-deficient mice

2022-11-29 | GSE198967 | GEO

Single-cell TCR transcriptomics of thymic iNKT cells from BALB/c and Cd80/Cd86 -/- (B7KO) mice

Project description:Single-cell TCR-seq analysis of murine thymic iNKT cells from three independent BALB/c mice and three independent Cd80/Cd86 (B7)-deficient mice

2022-11-29 | GSE198966 | GEO

Global transcriptional profiling reveals distinct functions of thymic stromal subsets and age-related changes during thymic involution

2014-09-12 | GSE56928 | GEO

Global transcriptional profiling reveals distinct functions of thymic stromal subsets and age-related changes during thymic involution

Project description:The thymic microenvironment is essential for proper differentiation and selection of thymocytes.Thymic involution in aged mice results in decreased T cell output and immune function. Here we use gene expression profiling of FACS sorted thymic stromal subsets to identify molecular mediators of thymocyte: stromal cell interactions, as well as gene expression changes thymic stromal subsets during early stages of thymic involution . We used microarrays to analyze gene expression differences between thymic stromal subsets from male C57BL/6J mice 1, 3, and 6 months of age. Thymic stromal subsets (cTEC, mTEClo, mTEChi, Sirpa-DC, Sirpa+DC, and fibroblasts) were isolated from two 1-, 3-, and 6- month old male C57BL/6J mice. After enzymatic digestion of the thymi, the stromal cells were FACS purified, and RNA was extracted, amplified, labeled and hybridized to Affymetrix mouse 430 2.0 arraysarrays. Raw data were uploaded to Gene Expression Commons for normalization. Both raw CEL and normalized datasets from the 36 samples are included. A model within Gene Expression Commons has been created for analyses/comparisons of these datasets, along with previously reported thymocyte subset datasets. The model within Gene Expression Commons thus contains 6 thymic stromal populations, each from mice 1, 3, and 6 months of age, with duplicates for each datset.

2014-09-12 | E-GEOD-56928 | biostudies-arrayexpress

TCR signal strength controls thymic differentiation of iNKT cell subsets

Project description:Three major phenotypically and functionally distinct invariant Natural Killer T (iNKT) cell subsets (iNKT1, iNKT17 and iNKT2), each with propensity to traffic to different tissues and to secrete different cytokines upon activation, have been defined. These fate assignments can be conferred upon iNKT cells during development in the thymus, but the cues that direct these decisions remain unclear. Here, we show that T cell antigen receptor (TCR) signal strength governs the development of iNKT cell subsets in the thymus, with high signaling strength necessary for iNKT2 and iNKT17 development. Alteration of TCR diversity and/or signaling dramatically diminished iNKT2 and iNKT17 cell subset development in a cell intrinsic manner. Decreased TCR signaling affected the persistence of Egr2 expression and the upregulation of PLZF both in vivo and in vitro. Genome-wide chromatin accessibility analysis revealed subset-specific activity of regulatory elements associated with unique signatures of transcription factor binding sites. NFAT and Egr binding motifs were found preferentially enriched in chromatin regulatory regions specifically accessible in iNKT2 cells that were lost in iNKT2 cells that had developed with reduced TCR signaling. Altogether, these data suggest a model of iNKT cell subset development where variable TCR signaling induces changes in chromatin accessibility at NFAT and Egr binding sites which exerts a determinative influence on the dynamic of gene enhancer accessibility that affects the developmental fate of iNKT cells.

2018-05-18 | GSE111427 | GEO

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