Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference

ABSTRACT: Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference

PROVIDER: PRJNA820742 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference

Project description:We subdivided circulating CD4+CD8+ double positive T cells, known to be associated with various disease environments, into several subtypes through single-cell RNA sequencing, and analyzed transition in transcriptome using trajectory analysis.

2022-03-30 | GSE199564 | GEO

Cellular heterogeneity of circulating CD4+CD8+ double positive T cells characterized by single-cell RNA sequencing

Project description:Cellular heterogeneity of circulating CD4+CD8+ double positive T cells characterized by single-cell RNA sequencing

| PRJNA762084 | ENA

Cellular heterogeneity of circulating CD4+CD8+ double positive T cells characterized by single-cell RNA sequencing

Project description:We subdivided circulating CD4+CD8+ double positive T cells, which are known to be related to various disease environments, into several subtypes through single-cell RNA sequencing, and compared gene signatures according to CD4 and CD8 protein expression levels using CD4 and CD8 antibody derived tags (feature barcode).

2021-10-27 | GSE183835 | GEO

Endothelial cell heterogeneity in pathological angiogenesis characterized by metabolic transcriptome diversity

Project description:Endothelial cell (EC) metabolism regulates angiogenesis and is an emerging target for anti-angiogenic therapy in tumor and choroidal neovascularization (CNV). In contrast to tumor ECs (TECs), CNV-ECs cannot be isolated for unbiased metabolic target discovery. Here we used scRNA-sequencing to profile 28,337 choroidal ECs (CECs) from mice to in silico distinguish healthy CECs from CNV-ECs. Trajectory inference suggested that CNV-ECs plastically upregulate genes in central carbon metabolism and collagen biosynthesis during differentiation from quiescent postcapillary venous ECs. CEC-tailored genome scale metabolic modeling predicted essentiality of SQLE and ALDH18A1 for proliferation and collagen production, respectively. Comparative analysis in TECs revealed more outspoken metabolic transcriptome heterogeneity in subtypes and consistent upregulation of SQLE and ALDH18A1 across tumor types. Inhibition of SQLE and ALDH18A1 reduced sprouting angiogenesis in vitro. These findings demonstrate the potential of integrated scRNA-seq analysis to identify angiogenic metabolic targets in disease ECs.

2020-06-25 | E-MTAB-8119 | biostudies-arrayexpress

Endothelial cell heterogeneity in pathological angiogenesis characterized by metabolic transcriptome diversity

Project description:Endothelial cell (EC) metabolism is an emerging target for anti-angiogenic therapy in tumor and choroidal neovascularization (CNV), but little is known about individual EC metabolic transcrip-tomes. Here, by scRNA-sequencing 28,337 murine choroidal ECs (CECs) and sprouting CNV-ECs, we constructed a taxonomy to characterize their heterogeneity. Comparison with murine lung tumor ECs (TECs) revealed congruent marker gene expression by distinct EC phenotypes across tissues and diseases, suggesting similar angiogenic mechanisms. Trajectory inference of CNV-ECs revealed that differentiation of venous to angiogenic ECs was accompanied by metabolic transcriptome plasticity. EC phenotypes displayed metabolic transcriptome heterogeneity. Hypothesizing that conserved genes are more important, we used an integrated analysis, based on congruent transcriptome analysis, CEC-tailored genome scale metabolic modeling, and gene expression me-ta-analysis in multiple cross-species datasets, followed by functional validation, to identify the top-ranking metabolic targets SQLE and ALDH18A1, involved in EC proliferation and collagen production, respectively, as novel angiogenic targets.

2020-03-31 | E-MTAB-8604 | biostudies-arrayexpress

Cellular heterogeneity of circulating CD4<sup>+</sup>CD8<sup>+</sup> double-positive T cells characterized by single-cell RNA sequencing.

Project description:Circulating CD4+CD8+ double-positive (DP) T cells are associated with a variety of disease states. However, unlike conventional T cells, the composition of this population is poorly understood. Here, we used single-cell RNA sequencing (scRNA-seq) to analyze the composition and characteristics of the DP T cell population circulating in the peripheral blood of cynomolgus monkeys. We found that circulating DP T cells not only contain a large number of naïve cells, but also comprise a heterogeneous population (CD4 CTL-, Eomes+ Tr1-, Th2-, Th17-, Tfh-, Treg-, CD8 CTL-, and innate-like cells) with multiple potential functions. Flow cytometry analysis revealed that a substantial number of the naïve DP T cells expressed CD8αβ, as well as CD8αα, along with high expression of CD31. Moreover, the CD4hiCD8lo and CD4hiCD8hi populations, which express high levels of the CD4 coreceptor, comprised subsets characterized by helper and regulatory functions, some of which also exhibited cytotoxic functions. By contrast, the CD4loCD8hi population with high CD8 coreceptor expression comprised a subset characterized by CD8 CTL- and innate-like properties. Taken together, the data show that scRNA-seq analysis identified a more diverse subset of the circulating DP cells than is currently known, despite this population being very small.

| S-EPMC8655006 | biostudies-literature

Characterization of circulating PDGFRa positive cells in fetus

Project description:Mesenchymal stem/stromal cells (MSCs) are supplied to the damaged tissue via circulation when the injury is massive. MSCs recruited to the damaged tissues support tissue regeneration by differentiating into parenchyma cells and suppressing inflammation. However, most of the analysis of the circulating MSCs have been conducted in adult models, the existence and properties in fetal circulation was not known. Here, we have extensively analyzed the circulating MSCs cells during development.

2020-04-16 | GSE126067 | GEO

Characterization of circulating PDGFRa positive cells in fetus

Project description:Characterization of circulating PDGFRa positive cells in fetus

| PRJNA520915 | ENA

Inference and validation of predictive gene networks from biomedical literature and gene expression data

Project description:Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. Using this framework we are able to show that network inference based on integration of prior knowledge derived from the biomedical literature with genomic data significantly improves the quality of inferred networks relative to other approaches. Our results also suggest that cell line experiments can be used to quantitatively assess the quality of networks inferred from tumor samples. Knock-down of eight genes were performed on colorectal cancer cell lines to identify the genes whose expression was significantly affected. These genes were subsequently used to validate the quality of our causal gene interaction network.

2013-12-23 | E-GEOD-53091 | biostudies-arrayexpress

Expression data from human OC+BAP+ double positive versus OC-BAP- double negative cells

Project description:Subpopulation of circulating monocyte/macrophage lineage cells show a calcifying ability in vivo and in vitro. These cells may contribute to intimal calcification within atherosclerotic lesions and may have pathophysiological clinical and therapeutic implication in vascular disorders. Such cells express Osteocalcin (OC) and Bone Alkaline Phosphatase (BAP). We analysed the expression profile of human OC+BAP+ cells versus OC-BAP- cells We compared three biological repilcates of OC+BAP+ versus OC-BAP- (each population coming from the same donor), each of the three coming from different healthy non diabetic donors.

2013-05-17 | E-GEOD-47060 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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