Epigenomic profiling of heart tissue in mammalian species
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51716 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9289420.fastq.gz | Fastqsanger.gz | |||
| ERR9289430.fastq.gz | Fastqsanger.gz | |||
| ERR9289440_1.fastq.gz | Fastqsanger.gz | |||
| ERR9289440_2.fastq.gz | Fastqsanger.gz | |||
| ERR9289450_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 213 |
Similar Datasets
Project description:Structural birth defects are the leading cause of infant mortality in the US and Europe. Among these, congenital heart disease (CHD) is the most common. Historically, Xenopus, mouse, and pig have provided models for CHD. However, it remains unknown what proteins and pathways are conserved between these species and human. Furthermore, the proteome driving the differences between three-chambered (Xenopus) and four-chambered (mammalian) hearts is unknown. Comparative proteomics of heart tissue from species at different evolutionary points can reveal molecular processes underlying heart function. We examined heart tissue proteomes of Xenopus tropicalis, Xenopus laevis, Mus musculus, and Sus scrofa and assessed protein expression changes in the context of pathways and protein complexes, and enrichment of corresponding genes in human heart diseases.
2019-08-01 | PXD009577 | Pride
Project description:RPL3L-containing ribosomes modulate mitochondrial activity in the mammalian heart.
| PRJEB49255 | ENA
Project description:Lifespan varies both within and across species, but the general principles of its control are not understood. To identify transcriptomic signatures of mammalian longevity, we sequenced multiple organs of young adult mammals corresponding to 8 different species, including Canadian beaver, long-tailed macaque, greater tube-nosed bat, baboon, white-footed mouse, sugar glider, Siberian chipmunk and American black bear. We aggregated this dataset with publicly available pan-mammalian data and performed multi-tissue gene expression analyses across 41 mammalian species. This allowed us to identifiy signatures of species longevity and assess their relationship with biomarkers of aging and lifespan-extending interventions. This dataset complements RNAseq profiles of tissues from 23 mammalian species stored at GSE43013.
2023-06-01 | GSE227359 | GEO
Project description:Sphingolipid metabolism controls mammalian heart regeneration
| PRJNA747264 | ENA
Project description:Global epigenomic reconfiguration during mammalian brain development
| PRJNA208503 | ENA
Project description:Epigenomic Atlas of Embryonic Human Heart Development
| PRJNA566407 | ENA
Project description:Development and function of the human heart depend on the dynamic control of tissue-specific gene expression by distant-acting transcriptional enhancers. While large numbers of heart enhancers have been identified using the mouse as a model system, many of these regulatory sequences are poorly conserved in the human genome. To generate an accurate genome-wide map of human heart enhancers, we used an epigenomic enhancer discovery approach and identified ~6,200 candidate enhancer sequences directly from fetal and adult human heart tissue. Consistent with their predicted function, these elements were markedly enriched near genes implicated in heart development, function and disease. To further validate their in vivo enhancer activity, we tested 65 of these human sequences in a transgenic mouse enhancer assay and observed that 43 (66%) drove reproducible reporter gene expression in the heart. These results support the discovery of a genome-wide set of non-coding sequences highly enriched in human heart enhancers which is likely to facilitate down-stream studies of the role of enhancers in development and pathological conditions of the heart. Examination of AcCBP/p300 binding in human adult heart, human fetal (16wk) heart and mouse postnatal day 2 heart
2011-12-04 | E-GEOD-32587 | biostudies-arrayexpress
Project description:FASILOX analysis of heart and lung tissue form mice with heart failure with preserved ejection fraction and several comorbidities.
2024-10-02 | PXD056447 | JPOST Repository
Project description:Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes. To study mammalian transcriptome evolution at high resolution, we generated RNA-Seq data (∼3.2 billion Illumina Genome Analyser IIx reads of 76 base pairs) for the polyadenylated RNA fraction of brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart, kidney, liver and testis (usually from one male and one female per somatic tissue and two males for testis) from nine mammalian species: placental mammals (great apes, including humans; rhesus macaque; mouse), marsupials (gray short-tailed opossum) and monotremes (platypus). Corresponding data (∼0.3 billion reads) were generated for a bird (red jungle fowl, a non-domesticated chicken) and used as an evolutionary outgroup.
2011-10-12 | E-GEOD-30352 | biostudies-arrayexpress
Project description:Development and function of the human heart depend on the dynamic control of tissue-specific gene expression by distant-acting transcriptional enhancers. While large numbers of heart enhancers have been identified using the mouse as a model system, many of these regulatory sequences are poorly conserved in the human genome. To generate an accurate genome-wide map of human heart enhancers, we used an epigenomic enhancer discovery approach and identified ~6,200 candidate enhancer sequences directly from fetal and adult human heart tissue. Consistent with their predicted function, these elements were markedly enriched near genes implicated in heart development, function and disease. To further validate their in vivo enhancer activity, we tested 65 of these human sequences in a transgenic mouse enhancer assay and observed that 43 (66%) drove reproducible reporter gene expression in the heart. These results support the discovery of a genome-wide set of non-coding sequences highly enriched in human heart enhancers which is likely to facilitate down-stream studies of the role of enhancers in development and pathological conditions of the heart.
2011-12-04 | GSE32587 | GEO