Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigating human T cell development in the human pediatric thymus using scRNA-seq

ABSTRACT: To study human T cell development at the single cell level we profiled thymocytes from 3 pediatric donors using scRNA-seq. The data was subsequently used in the construction of a cell atlas of human thymic development across the life span. This allowed the identification of over 50 cell states in the human thymus and helped map the developmental trajectories of conventional and unconventional T cells throughout development.

ORGANISM(S): Homo sapiens

PROVIDER: GSE206710 | GEO | 2022/06/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Investigating human T cell development in the human pediatric thymus using scRNA-seq

Project description:Investigating human T cell development in the human pediatric thymus using scRNA-seq

| PRJNA851794 | ENA

Single-cell RNA sequencing resolves cellular heterogeneity throughout embryonic development of the thymus

Project description:This dataset consists of single-cell RNA-seq (Drop-seq) data from eight days of mouse thymus development. Samples span from embryonic day 12.5, when the thymus coalesces, until birth. They cover the whole thymus, including mesenchyme, endothelium, epithelium, thymocytes, and other lymphocytes. The dataset also includes Drop-seq data on Rag1-/- embryos and on fetal thymic organ cultures (control and a retinoic acid perturbation).

2018-06-05 | GSE107910 | GEO

Single-cell RNA-seq of mouse thymus iNKT cells

Project description:Invariant natural killer T cells (iNKT) cells are innate-like T cells, selected from thymic cortex-resident CD4+CD8+ double positive (DP) thymocytes. Despite major advances in the understanding of iNKT cells development, the heterogeneity of iNKT subsets and underlying molecular programs that guide iNKT cell-lineage remain unclear.

2022-08-10 | GSE130184 | GEO

The human fetal thymus generates effector invariant γδ T cells in a Lin28b-dependent manner

Project description:In the mouse thymus, invariant γδ T cells are generated at well-defined times during development and acquire effector functions before exiting the thymus. However, whether such thymic programming can occur in human is not known. Here we analyzed human fetal and post-natal γδ thymocytes and investigated the role of hematopoietic-stem-and-precursor-cells (HSPC) in the generation of human γδ T cells. Unlike post-natal γδ thymocytes, fetal γδ thymocytes were functionally programmed (e.g. IFNγ, granzymes), expressed low levels of terminal-deoxynucleotidyl-transferase (TdT) and were highly enriched for invariant/public germline-encoded CDR3 sequences (TRGV8-TRJP1-CATWDTTGWFKIF, TRDV2-TRDD3-CACDTGGY and TRDV1-TRDD3-CALGELGD, previously shown to be expanded in cytomegalovirus infection) composed of short-homology-repeat-containing gene segments. Furthermore, these unique characteristics were due to an intrinsic property of fetal HSPC caused by high expression of the RNA-binding protein Lin28b. In conclusion, our data indicate that the human fetal thymus generates, in a HSPC/Lin28b-dependent manner, invariant γδ T cells with programmed effector functions.

2019-11-21 | GSE128163 | GEO

Tcf-1 expression in murine thymus

Project description:The DNA binding factor Tcf-1 is one of the most prominently expressed genes in thymocytes yet it's global DNA binding pattern remained unknown. Here we have assessed by ChIP-seq the Tcf-1 binding pattern in murine thymocytes. Tcf-1 ChIP-seq of 1 sample and input control.

2013-06-12 | E-GEOD-46662 | biostudies-arrayexpress

Expression data from immature V2 and DP cells in the thymus of Sox4 conditional knockout mice and wild type mice

Project description:To determine Sox4 function during intrathymic αβ T cell development, global transcriptome analysis was performed and suggested a deficit in miR181 expression in Sox4-deficient DP thymocytes.

2018-09-26 | GSE120477 | GEO

Unraveling human T cell development using scRNA-seq

Project description:T cells develop in the thymus from multipotent lymphoid precursors. During this gradual differentiation process thymocytes go through several decision points, before they fully mature into conventional and unconventional T cells. The underlying molecular mechanisms have been investigated in mice, but several details remain unclear in the human context. To be able to study the drivers of thymocyte differentiation in human, we have generated several 3' scRNA-seq libraries from enriched thymocyte populations.

2022-07-14 | GSE205439 | GEO

Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes

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.

2020-04-17 | GSE144870 | GEO

Expression data from DP cells in the thymus of SRSF1-null and wild type mice

Project description:iNKT cells are highly conserved innate-like T lymphocytes that develop from CD4+CD8+ DP cells. It remains largely unknown whether post-transcriptional regulation has critical roles in iNKT cells. Here we show conditional deactivation of SRSF1 in DP thymocytes impaired iNKT cell development and survival in a cell-intrinsic manner.

2022-08-11 | GSE156013 | GEO

A single cell analysis of porcine thymopoiesis and thymic iNKT cells

Project description:Many aspects of the porcine immune system remain poorly characterized which poses a barrier to improving swine health and utilizing pigs as preclinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to create a cell atlas of the postnatal pig thymus. Our data found conserved features as well as species-specific differences in cell states and cell types compared to human thymocytes. We also describe several unconventional T cell types with gene expression profiles associated with innate effector functions. This includes a cell census of >11,000 differentiating invariant natural killer T (iNKT) cells, which revealed that the functional diversity of pig iNKT cells differs substantially from the paradigm of iNKT0/1/2/17 subset differentiation established in mice. Collectively, our data characterizes key differentiation events in porcine thymopoiesis and iNKT cell maturation, which provide new insights into pig T cell development.

2022-08-04 | GSE192520 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data