WAVE_WGS - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009696 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We previously identified somatic activating KRAS mutations in a majority of human arteriovenous malformations (AVMs), using whole exome sequencing, which were enhanced in AVM endothelial cell fractions. We have now performed whole genome sequencing on AVM endothelial and non-endothelial cell fractions, as well as paired blood samples, in order to identify further somatic mutations.
| EGAS00001006719 | EGA
Project description:To understand the molecular mechanisms during the maturation of cord blood-derived endothelial cells into blood brain barrier capillary endothelial cells (BCECs), we have employed whole genome microarray expression profiling to identify genes responsible for the maturation process. Hematopoietic stem cells were isolated from cord-blood samples and differentiated into endothelial cells. The endothelial cells were further maturated into BCECs by co-culturing with blood-brain barrier (BBB) specific cells (pericytes) for 3 days and 6 days.
2013-10-18 | GSE45171 | GEO
Project description:Tissue differences are one of the largest contributors to variability in the human DNA methylome. Despite the tissue specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well documented. Here we aimed to provide a resource to the community to aid interpretation of blood based DNA methylation results in the context of brain tissue. We used paired samples from 16 individuals from three brain regions and whole blood, run on the Illumina 450K Human Methylation Array to quantify the concordance of DNA methylation between tissues. From these data we have made available metrics on: the variability of CpGs in our blood and brain samples, the concordance of CpGs between blood and brain, and estimations of how strongly a CpG is affected by cell composition in both blood and brain through the web application BECon (Blood-Brain Epigenetic Concordance; https://redgar598.shinyapps.io/BECon/). We anticipate that BECon will enable biological interpretation of blood based human DNA methylation results, in the context of brain.
2017-08-01 | GSE95049 | GEO
Project description:To understand the molecular mechanisms during the maturation of cord blood-derived endothelial cells into blood brain barrier capillary endothelial cells (BCECs), we have employed whole genome microarray expression profiling to identify genes responsible for the maturation process. Hematopoietic stem cells were isolated from cord-blood samples and differentiated into endothelial cells. The endothelial cells were further maturated into BCECs by co-culturing with blood-brain barrier (BBB) specific cells (pericytes) for 3 days and 6 days. The gene expression in human hematopoietic stem cell-derived endothelial cells was measured at 3 and 6 days after co-culture with pericytes. Three independent experiments were performed at each time (3 or 6 days). The RNA obtained from different experiments were pooled together for each group before microarray studies.
2013-10-18 | E-GEOD-45171 | biostudies-arrayexpress
Project description:Brain microvessels form the blood-brain barrier, and are dysfunctional in several neurological disorders. Brain microvessels are formed by brain microvascular endothelial cells (BMECs) and pericytes, and the molecular constituents of these cell types remain incompletely characterized, especially in humans. To improve molecular knowledge of these cell types and identify species differences in gene expression, we performed RNA-sequencing on brain microvessels isolated from human and mouse tissue samples using laser capture microdissection. We also performed RNA-sequencing of matched whole brain samples to identify genes with microvessel-enriched expression.
2020-07-23 | GSE142209 | GEO
Project description:Gene expression profiles of various isolated normal and tumour cell types The goal was to identify genes differentially expressed in different cell types between normal and tumour tissues. To this end, different cell types (endothelial cells, macrophages and epithelial cells) were isolated from non-paired primary normal colon tissues and colorectal carcinomas and subsequently RNA was isolated. Endothelial cells and epithelial cells were isolated using facs-sorting, whereas macrophages were isolated by means of plastic adherence. For comparison RNA was also isolated from non-paired whole normal colon tissue and whole tumour colorectal carcinomas (so called “bulk”). RNA was processed and hybridized onto Agilent microarrays. Primary goal was to establish an endothelial cell genetic profile. For this we compared the gene expression of tumour endothelial cells (TECs) with normal endothelial cells (NECs).
2016-10-29 | GSE89287 | GEO
Project description:Each organ of the human body requires locally-adapted blood vessels1–3. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model, we reveal a molecular mechanism for brain-specific angiogenesis that operates under the control of Wnt7a/b ligands, well-known blood-brain barrier maturation signals4–6. The control mechanism relies on Wnt7a/b-dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI-anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane which lines the brain surface, and whose distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically, Mmp25 confers brain invasive competence by cleaving the pial basement membrane-enriched Col4a5/6 within a short non-collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition, the Wnt/β-catenin-dependent organotypic control of brain angiogenesis is lost, resulting in a properly patterned, yet blood-brain barrier-defective cerebrovasculature. This work reveals an organ-specific angiogenesis mechanism, sheds light on tip cell mechanistic angiodiversity, and thereby illustrates how organs, by imposing local constraints on angiogenic tip cells, can select vessels matching their distinctive physiological requirements.
2024-02-08 | PXD042613 | Pride
Project description:RNAseq from Illumina MiSeq 75bp paired end for transcriptome assembly. The following tissue samples were pooled: skeletal muscle; kidney; spleen; ovaries; placenta; castor gland; tail; toe webbing; whole blood; brain; lung; liver; heart; stomach; tongue; intestine
2017-12-24 | E-MTAB-6258 | biostudies-arrayexpress
Project description:Differential host responses in coronavirus disease 2019 (COVID-19) and multisystem inflammatory syndrome in children (MIS-C) remain poorly characterized. Here we use next-generation sequencing to longitudinally analyze blood samples from pediatric patients with acute COVID-19 (n=70) or MIS-C (n=141) across three hospitals. Profiling of plasma cell-free nucleic acids uncovers distinct signatures of cell injury and death between COVID-19 and MIS-C, with increased multi-organ involvement in MIS-C encompassing diverse cell types including endothelial and neuronal cells, and an enrichment of pyroptosis related genes. Whole blood RNA profiling reveals upregulation of similar pro-inflammatory pathways in COVID-19 and MIS-C, but also MIS-C specific downregulation of T cell-associated pathways. Profiling of plasma cell-free RNA and whole blood RNA in paired samples yields different yet complementary signatures for each disease state. Our work provides a systems-level view of immune responses and tissue damage in COVID-19 and MIS-C and informs the future development of new disease biomarkers.
2023-06-04 | GSE225221 | GEO
Project description:Differential host responses in coronavirus disease 2019 (COVID-19) and multisystem inflammatory syndrome in children (MIS-C) remain poorly characterized. Here we use next-generation sequencing to longitudinally analyze blood samples from pediatric patients with acute COVID-19 (n=70) or MIS-C (n=141) across three hospitals. Profiling of plasma cell-free nucleic acids uncovers distinct signatures of cell injury and death between COVID-19 and MIS-C, with increased multi-organ involvement in MIS-C encompassing diverse cell types including endothelial and neuronal cells, and an enrichment of pyroptosis related genes. Whole blood RNA profiling reveals upregulation of similar pro-inflammatory pathways in COVID-19 and MIS-C, but also MIS-C specific downregulation of T cell-associated pathways. Profiling of plasma cell-free RNA and whole blood RNA in paired samples yields different yet complementary signatures for each disease state. Our work provides a systems-level view of immune responses and tissue damage in COVID-19 and MIS-C and informs the future development of new disease biomarkers.
2023-06-04 | GSE225220 | GEO