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Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells - tuft and non-tuft cells

ABSTRACT: Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells - tuft and non-tuft cells

PROVIDER: PRJNA938786 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23620993_1.fastq.gz	Fastqsanger.gz
	SRR23620993_2.fastq.gz	Fastqsanger.gz
	SRR23620994_1.fastq.gz	Fastqsanger.gz
	SRR23620994_2.fastq.gz	Fastqsanger.gz
	SRR23620995_1.fastq.gz	Fastqsanger.gz

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Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells - tuft and non-tuft cells

Project description:The network of thymic stromal cells provides essential niches with unique molecular cues controlling T-cell development and selection. Recent single-cell RNA-sequencing studies uncovered a large transcriptional heterogeneity among thymic epithelial cells (TEC) demonstrating a previously unappreciated complexity. However, there are only very few cell markers that allow a comparable phenotypic identification of TEC. Here we deconvoluted by massively parallel flow cytometry and machine learning known and novel TEC phenotypes into novel subpopulations and related these by CITEseq to the corresponding TEC subtypes defined by the cells’ individual RNA profiles. This approach phenotypically identified perinatal cTEC, physically located these cells within the cortical stromal scaffold, displayed their dynamic change during the life course and revealed their exceptional efficiency in positively selecting immature thymocytes. Collectively, we have identified novel markers that allow for an unprecedented dissection of the thymus stromal complexity, the cells physical isolation and assignment of specific functions to individual TEC subpopulations.

2023-05-17 | GSE226128 | GEO

Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells

Project description:Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells

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Thymic tuft cell single-cell mRNA analysis

Project description:The goal of the study was to sequence mRNA from tuft cells (identified as CD11c-;CD45-;EpCAM+;IL-25+ using Flare25 reporter mice) in C57BL/6 and Aire-/- mice. The data were used to investigate thymic tuft cell heterogeneity with and without AIRE protein expression.

2018-06-03 | GSE114895 | GEO

Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells

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Thymic tuft cell single-cell mRNA analysis

Project description:Thymic tuft cell single-cell mRNA analysis

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Intestinal and thymic tuft cell RNA-seq

Project description:Intestinal and thymic tuft cell RNA-seq

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Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells.

Project description:The network of thymic stromal cells provides essential niches with unique molecular cues controlling T cell development and selection. Recent single-cell RNA sequencing studies have uncovered previously unappreciated transcriptional heterogeneity among thymic epithelial cells (TEC). However, there are only very few cell markers that allow a comparable phenotypic identification of TEC. Here, using massively parallel flow cytometry and machine learning, we deconvoluted known TEC phenotypes into novel subpopulations. Using CITEseq, these phenotypes were related to corresponding TEC subtypes defined by the cells' RNA profiles. This approach allowed the phenotypic identification of perinatal cTEC and their physical localisation within the cortical stromal scaffold. In addition, we demonstrate the dynamic change in the frequency of perinatal cTEC in response to developing thymocytes and reveal their exceptional efficiency in positive selection. Collectively, our study identifies markers that allow for an unprecedented dissection of the thymus stromal complexity, as well as physical isolation of TEC populations and assignment of specific functions to individual TEC subtypes.

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Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [ex_vivo_tuft]

Project description:The goal of this study was to determine whether thymic tuft cells activation during acute thymic involution is mediated by IL-13, which is produced by ILC2 upon involution and the receptor for which is expressed by tuft cells. For this purpose we sorted thymic tuft cells from WT mice, treated them ex vivo with recombinant IL-13 for 24 hours, and performed bulk RNA-Seq.

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Intestinal and thymic tuft cell RNA-seq

Project description:The goal of the study was to sequence mRNA from tuft cells (identified as CD45-;EpCAM+;IL-25+ using Flare25 reporter mice) in the epithelia of thymus and small intestine. As a control, non-tuft epithelial cells (CD45-;EpCAM+;IL-25-) were also isolated. The data were used to compare tuft cell markers between the small intestine and thymus.

2018-05-19 | GSE114668 | GEO

Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [Tuft_after_irr]

Project description:The goal of this study was to understand the role of thymic tuft cells in thymic regeneration following irradiation-induced acute involution. For this purpose we treated WT mice with sublethal irradiation, sorted tuft cells from their thymi 3 days after treatment when the thymus begins its recovery, and performed bulk RNA Seq.

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