Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Locus-specific and genome-wide analysis of adaptations to hypoxia in iPSC-derived endothelium from a population adapted to high altitude [scRNA-Seq]

ABSTRACT: Locus-specific and genome-wide analysis of adaptations to hypoxia in iPSC-derived endothelium from a population adapted to high altitude [scRNA-Seq]

PROVIDER: PRJNA1131467 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29700105.fastq.gz	Fastqsanger.gz
	SRR29700106.fastq.gz	Fastqsanger.gz
	SRR29700107.fastq.gz	Fastqsanger.gz
	SRR29700108.fastq.gz	Fastqsanger.gz
	SRR29700109.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Locus-specific and genome-wide analysis of adaptations to hypoxia in iPSC-derived endothelium from a population adapted to high altitude [scRNA-Seq]

Project description:Tibetan adaptation to high-altitude hypoxia remains a classic example of Darwinian selection in humans. Amongst Tibetans, alleles in the EPAS1 gene - whose protein product, Hif-2α, is a central regulator of the hypoxia response - have repeatedly been shown to carry some of the strongest signals of positive selection in humans and to influence several adaptive phenotypes. We recently showed that the selected haplotype at this locus spans a hypoxia-dependent enhancer (ENH5) that contributes to the regulation of EPAS1 in a variety of cell types. However, selective sweep signals alone may account for only part of the phenotypes that differentiate Tibetans from closely related lowlanders. Therefore, there is a pressing need to functionally probe adaptive alleles and their impact at the genome-wide level and across cell types to uncover the full range of beneficial traits. To cast a wider net, we established a library of induced pluripotent stem cells (iPSCs) derived from Tibetan and Han Chinese individuals, a robust model system allowing precise exploration of both locus-specific and genome-wide effects on transcriptional responses. We harness this system by differentiating the iPSC library into vascular endothelium and investigating the locus-specific effects of the ENH5 enhancer in this cellular context. In addition, we use it to explore Tibetan-specific transcriptome-wide responses and find evidence that energy metabolism and immune pathways have been shaped by natural selection in Tibetans. Finally, to aid with the interpretation of the transcriptional differences between populations, we test for polygenic adaptations as a complementary in silico approach for the identification of beneficial Tibetan phenotypes.

2024-12-01 | GSE271457 | GEO

Locus-specific and genome-wide analysis of adaptations to hypoxia in iPSC-derived endothelium from a population adapted to high altitude [RNA-Seq]

2024-12-01 | GSE271456 | GEO

Locus-specific and genome-wide analysis of adaptations to hypoxia in iPSC-derived endothelium from a population adapted to high altitude [RNA-Seq]

Project description:Locus-specific and genome-wide analysis of adaptations to hypoxia in iPSC-derived endothelium from a population adapted to high altitude [RNA-Seq]

| PRJNA1131465 | ENA

Transcriptomic analysis of iPSC-derived endothelium reveals adaptations to high altitude hypoxia in energy metabolism and inflammation

2025-01-12 | GSE280017 | GEO

Transcriptomic analysis of iPSC-derived endothelium reveals adaptations to high altitude hypoxia in energy metabolism and inflammation

Project description:Transcriptomic analysis of iPSC-derived endothelium reveals adaptations to high altitude hypoxia in energy metabolism and inflammation

| PRJNA1175738 | ENA

Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-dose Ultraviolet Radiation in High-altitude Environments

Project description:Tibetan chickens exhibit specific adaptations to high-altitude conditions compared with their lowland counterparts. To illustrate the genetic mechanisms of such adaptations in highland chickens, the genomes of four highland and four lowland chicken populations were resequenced. Our results showed that genes under positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune response, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of non-synonymous single nucleotide polymorphisms between highland and lowland populations was also analyzed by chi-square test. The results showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development, which were related to adaptations to hypoxia and intense radiation. RNA sequencing also revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Additionally, an evident admixture found in Tibetan chickens suggested a history of introgression from lowland gene pools. Overall, our data provided new insights into the unique adaptation of highland animals to extreme environments.

2016-01-26 | GSE77166 | GEO

Moderate hypoxia influence at intermediate altitude in Argentinean Andes

Project description:This study evaluates genetic and phenotypic variation in the intermediate altitude CalchaquÃ population living in the CalchaquÃ Valleys of the Argentinean Andes in the town of Cachi at 2300 m. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to moderate hypoxia at a intermediate altitude. DNA from 24 saliva samples of CalchaquÃes living at 2300 m in Cachi in the Province of Salta in Argentina was genotyped.

2014-04-05 | E-GEOD-56518 | biostudies-arrayexpress

Moderate hypoxia influence at intermediate altitude in Argentinean Andes

Project description:This study evaluates genetic and phenotypic variation in the intermediate altitude Calchaquí population living in the Calchaquí Valleys of the Argentinean Andes in the town of Cachi at 2300 m. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to moderate hypoxia at a intermediate altitude.

2014-04-05 | GSE56518 | GEO

Transcriptomic analysis of iPSC-derived endothelium reveals adaptations to high altitude hypoxia in energy metabolism and inflammation.

Project description:Tibetan adaptation to high-altitude hypoxia remains a classic example of Darwinian selection in humans. Amongst Tibetan populations, alleles in the EPAS1 gene - whose protein product, HIF-2α, is a central regulator of the hypoxia response - have repeatedly been shown to carry some of the strongest signals of positive selection in humans. However, selective sweep signals alone may only account for some of the phenotypes that differentiate high-altitude adapted populations from closely related lowlanders. Therefore, there is a pressing need to functionally probe adaptive alleles and their impact at both the locus-specific and genome-wide levels and across cell types to uncover the full range of beneficial traits. To this end, we established a library of induced pluripotent stem cells (iPSCs) derived from Tibetan and Han Chinese individuals, a robust model system allowing precise exploration of allelic effects on transcriptional responses, and we differentiated them into vascular endothelium. Using this system, we focus first on a hypoxia-dependent enhancer (ENH5) that contributes to the regulation of EPAS1 to investigate its locus-specific effects in endothelium. Then, to cast a wider net, we harness the same experimental system to compare the transcriptome of Tibetan and Han Chinese cells in hypoxia and find evidence that angiogenesis, energy metabolism and immune pathways differ between these two populations with different histories of long-term residence at high altitude. Coupled with evidence of polygenic adaptations targeting the same pathways, these results suggests that the observed transcriptional differences between the two populations were shaped by natural selection.

| S-EPMC11809796 | biostudies-literature

Transcriptional response to hypoxia in iPSC-derived endothelial cells from a high altitude adapted population

Project description:Transcriptional response to hypoxia in iPSC-derived endothelial cells from a high altitude adapted population

| PRJNA1153635 | ENA