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Human Early Postnatal Thymus [ATAC-seq]

ABSTRACT: Human Early Postnatal Thymus [ATAC-seq]

PROVIDER: PRJNA1103192 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28774078_1.fastq.gz	Fastqsanger.gz
	SRR28774078_2.fastq.gz	Fastqsanger.gz
	SRR28774079_1.fastq.gz	Fastqsanger.gz
	SRR28774079_2.fastq.gz	Fastqsanger.gz
	SRR28774080_1.fastq.gz	Fastqsanger.gz

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Human Early Postnatal Thymus [ATAC-seq]

Project description:Within the thymus, regulation of the cellular cross-talk directing T cell development is dependent on spatial interactions within specialized niches. To create a holistic, spatially defined map of tissue niches guiding postnatal T cell development we employed the multidimensional imaging platform CO-detection by indEXing (CODEX), as well as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Assay for Transposable-Accessible Chromatin (ATAC-seq). We generated age-matched 4–5-month-old postnatal thymus datasets for both male and female donors, and describe signaling and cell-cell interaction networks in sequential thymocyte developmental niches. Together, these data represent a unique age-matched spatial multiomic resource to investigate how sex-based differences in thymus regulation and T cell development arise, and provide an essential resource to understand the mechanisms underlying immune function and dysfunction in males and females.

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Project description:During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding precursors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis.

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Human Vg9Vd2 T cells develop within the postnatal thymus via a three-stage pathway defined by distinct molecular and cellular changes

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Project description:Gene expression analysis of early thymic progenitors and thymus seeding progenitors Eight distinct populations were analysed, each with between 2 and 6 biological replicates.

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