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ATAC-seq of FOXP3+ CD4SP regulatory T cells and their FOXP3- CD4SP conventional counterparts from the human thymus

ABSTRACT: ATAC-seq of FOXP3+ CD4SP regulatory T cells and their FOXP3- CD4SP conventional counterparts from the human thymus

PROVIDER: PRJEB49131 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR7454560_1.fastq.gz	Fastqsanger.gz
	ERR7454560_2.fastq.gz	Fastqsanger.gz
	ERR7454561_1.fastq.gz	Fastqsanger.gz
	ERR7454561_2.fastq.gz	Fastqsanger.gz
	ERR7454562_1.fastq.gz	Fastqsanger.gz

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RNA-seq of FOXP3+ CD4SP regulatory T cells and their FOXP3- CD4SP conventional counterparts from the human thymus

Project description:RNA-seq of FOXP3+ CD4SP regulatory T cells and their FOXP3- CD4SP conventional counterparts from the human thymus

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Project description:Recent studies have demonstrated that mature regulatory T cells ( Tregs) develop in the thymus via two pathways involving distinct Treg progenitors (TregP) - CD25+FOXP3- (CD25+ TregP) and CD25-FOXP3lo (FOXP3lo TregP) Treg progenitors. To examine this process in more detail we carried out single-cell RNA-Seq and TCR-Seq on sorted CD4+CD8+ double-positive (DP) thymocytes, CD4+ Ssingle -positive (CD4SP)P thymocytes, CD25+ TregP, FOXP3lo TregP, mature CD25+FOXP3+ Tregs and recirculating/long-term resident Tregs (RT-Tregs). Sorted populations were individually hashtagged and then combined into one scRNA-Seq/TCR-Seq library before sequencing and subsequent analysis. We found that both CD25+ TregP and FOXP3lo TregP arise via an initial agonist activated state that gives rise to a second transitional stage before differentiating into mature Tregs. Using both scRNA-Seq and bulk RNA-Seq on sorted thymocyte subsets we demonstrate that CD25+Foxp3- TregP are significantly enriched for Il2 production, suggesting that they are the major source of IL-2 needed to convert TregP into mature Tregs. Using TCR-Seq we found that several TCRs were clearly biased in favor of the conventional or Treg lineages, but that a large fraction of TCRs were found in both these lineages. Finally, we found that recirculating/resident Tregs in the thymus are not monomorphic, but are composed of multiple distinct subsets and that these RT-Tregs express the most diverse TCR repertoire of all CD4SP thymcocytes. Thus, our studies define multiple stages of Treg differentiation within the thymus, and serve as a resource for future studies on CD4+ thymocyte development and Treg differentiation.

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Comparative proteomic analysis of mouse CD4+Foxp3+ regulatory T cells and CD4+Foxp3- conventional T cells

Project description:In this study, we compared the proteomes of mouse CD4+Foxp3+ regulatory T cells (Treg) and CD4+Foxp3- conventional T cells (Tconv) in order to build a data set of proteins differentially regulated in these two cell populations. The data set contains mass spectrometry results from the analysis of 7 biological replicates of Treg/Tconv cell samples purified by flow cytometry, each experiment performed from a pool of 4-5 mice. Global proteomic analysis of each sample was performed by single-run nanoLC-MS/MS, using chromatographic separation of peptides on 50cm C18 reverse-phase columns, with either a 480min gradient on LTQ-Velos orbitrap mass spectrometer (replicates 1 and 2) or a 300min gradient on Q-Exactive orbitrap mass spectrometer (replicates 3-7). Several MS injection replicates were performed for some experiments, leading to 27 raw files composing the data set. The detailed description of each analysis (file name, sample type, biological replicate number, MS technical replicate number, MS instrument used, sample name in MaxQuant ouput) is given in the table “Files list.txt”.

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RNA-seq of FOXP3+ CD4SP regulatory T cells and their FOXP3- CD4SP conventional counterparts from the human thymus

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