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:Blood-brain barrier role in metabolite regulation via excitatory amino acid transporter 3. The questions we would like to address are: What are the metabolomic changes in whole brain regions and blood-brain barrier compartments with and without endothelial cell-specific slc1a1 glutamate transporter? Are these differences pulled out or exacerbated by mimicking an excess extracellular glutamate state using a subseizure dose of Kainic Acid? Cortex, hypothalamus, and cerebellum were isolated as well as whole brain, enriched microvessels, and plasma fractions from slc1a1 (EAAT3) endothelial cell-specific conditional knockout mice. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA). LC-MS/MS data acquired in positive mode.
2025-03-25 | MSV000097449 | GNPS
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:Dysfunctional brain barriers contribute to the pathophysiology of chronic CNS diseases, but few non-viral technologies are established that effectively target these interfaces. In this work, we developed a lipid-siRNA conjugate that modulate gene expression in brain barriers such as the blood-brain-barrier (BBB), which describes the restrictive properties of brain microvascular endothelial cells (BMEC), as well as the blood-CSF-barrier (BCSFB) formed by the choroid plexus. We showed robust delivery and knockdown in brain endothelial cells and the choroid plexus. In this experiment, we used single cell RNA sequencing to determine which CNS cell types exhibit siRNA-mediated gene silencing. To that end, we administered a 20 mg/kg intravenous dose of our lipid siRNA conjugate targeting Ppib or a non-targeting control. Brains were dissociated into single cells and processed for sequencing using PIPseq workflow. We found that gene silencing was specific to the brain barriers; we only detected knockdown in brain endothelial and choroid plexus epithelial cells.
2025-04-02 | E-MTAB-14840 | biostudies-arrayexpress
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:MicroRNA expression profling from 14 adult whole blood samples with flow cytometry cell fractions
| PRJNA1117491 | ENA
Project description:The low permeability and high selectivity of the blood vessels of the brain and central nervous system (CNS) characterize the blood-brain barrier (BBB). Tight junctions, a lack of fenestrations, and low rates of transcytosis in the endothelial cells of the vasculature prevent passive diffusion of most molecules other than water, gases and some lipid soluble molecules (Obermeier, Daneman, & Ransohoff, 2013). Any additional nutrients must be transported across the barrier with the help of transporter proteins. Two protein families account for most transporters. ABC transporters use ATP to power primary-active transport to move molecules across the BBB against an electrochemical gradient, frequently excluding drugs from entering the brain. Some SLC transporters facilitate transport of solutes along an electrochemical gradient, while others permit secondary-active transport by coupling the flow of a solute traveling down the electrochemical gradient to power another solute against its electrochemical gradient. Brain microvessel endothelial cells (BMEC) from human cerebral cortex were enriched through a homogenization and centrifugation procedure. Two BMEC and two tissue were sequenced with paired-end reads on a SOLiD 5500 Wildfire. Raw data was aligned using LifeScope Genomic Analysis, gene expression determined through Cufflinks, and splice junctions identified by aligning to a custom database of known to known and known to novel junctions. We found numerous examples of transporters with enriched expression in the isolated BMECs compared to whole brain tissue. In total, 131 transporter genes or pseudogenes (109 SLC, 22 ABC) are enriched at least 1.25 fold in BMEC enriched samples, and 57 of these are enriched over 2-fold (50 SLC, 7 ABC). Thirteen genes were found to have at least twice as many counts in BMEC enriched samples than in whole tissue for at least one alternative splice junction. Inversely, 23 genes were found to have at least one alternative splice junction with half as many counts in BMEC enriched samples than in whole tissue.
2017-01-26 | GSE94064 | GEO