Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression responses to oxygen challenge in a panel of human brain organoids

ABSTRACT: The human brain is highly sensitive to oxygen availability, and hypoxia is a common risk factor for neurological and cognitive traits throughout life. Hypoxia exerts distinct effects on different brain cell types, many of which involve changes in gene expression. We used brain organoids derived from genotyped human iPSC lines to characterize gene expression at single-cell resolutions under normoxic conditions and both hypoxic and hyperoxic challenges.

ORGANISM(S): Homo sapiens

PROVIDER: GSE273907 | GEO | 2024/09/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNAseq of scWAT obtained from normoxic (21% oxygen) and hypoxic (10% oxygen) mice

Project description:Subcutaneous adipose tissue (scWAT) was collected from mice exposed to either 10% O2 or maintained under normoxic atmospheric conditions. 129Ev/Sv mice were housed in conventional cages from birth in a temperature- (23°C) and humidity-controlled environment with a 12 h photoperiod and given ad libitum access to standard rodent chow (RM1(E), Special Diet Services, UK) and water. At 7 weeks of age, mice were randomly assigned to remain under normoxic conditions, or transferred to a normobaric hypoxia chamber (10% O2; PFI systems, Milton Keynes, UK). Mice were maintained in hypoxia or normoxia for 28 days, after which they were killed by cervical dislocation. The scWAT was removed from the inguinal region, snap frozen and stored at -80°C until further analysis. The inguinal lymph node was removed from scWAT depots prior to RNA-seq analysis.

2023-10-01 | E-MTAB-12299 | biostudies-arrayexpress

Plasmodium falciparum

Project description:Plasmodium falciparum: hyperoxic vs normoxic conditions

| PRJNA121167 | ENA

Transcriptomic analysis of engineered cardiac tissue in an oxygen gradient

Project description:We report the use of RNA-seq for transcriptional analysis of engineered cardiac tissues cultured in microphysiological systems developed for tight control of oxygen levels, comparing normoxia, hypoxia, and a gradient divided into the normoxic side and hypoxic side.

2022-12-08 | GSE189108 | GEO

Transcriptional profile of Candida parapsilosis CLIB214 21% Oxygen (normoxia) versus at 1% oxygen (hypoxia).

Project description:Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis in hypoxic condition. RNA was isolated from CLIB214 grown in YPD medium in normoxia or hypoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. Isolates from normoxic condition were labeled with Cy3 and isolates from hypoxic condition were labeled with Cy5.

2011-11-30 | E-GEOD-32712 | biostudies-arrayexpress

In Vivo Protein Turnover Rates in Varying Oxygen Tensions Nominate MYBBP1A as a Novel Mediator of the Hyperoxia Response

Project description:Oxygen deprivation and excess are both toxic to mammals. Thus, the body’s ability to adapt to varying oxygen tensions is critical for survival. While the transcriptional response to acute hypoxia has been well-studied, the post-translational effects of hypoxia and hyperoxia have been underexplored. In this study, we systematically investigate protein turnover rates in mouse heart, lung, and brain under different inhaled oxygen tensions. We find that the lung proteome is the most responsive to changes in oxygen tension, likely due to the direct exposure of alveoli to inhaled oxygen. In particular, several extracellular matrix (ECM) proteins such as collagens and laminins, are stabilized in the lung under both hypoxia and hyperoxia, suggesting their post-translational regulation. Furthermore, we validate our previous finding that complex 1 of the electron transport chain (ETC) is destabilized in hyperoxia, explaining the exacerbation of associated disease models by hyperoxia and rescue by hypoxia. Moreover, we nominate MYBBP1A as a novel transcriptional regulator in hyperoxic lung, particularly in the context of rRNA homeostasis. Overall, our study highlights the importance of the effects of oxygen tensions on protein turnover rates and identifies novel tissue-specific mediators of oxygen-dependent responses.

2023-12-10 | GSE234123 | GEO

In Vivo Protein Turnover Rates in Varying Oxygen Tensions Nominate MYBBP1A as a Novel Mediator of the Hyperoxia Response

Project description:Oxygen deprivation and excess are both toxic to mammals. Thus, the ability to adapt to varying oxygen tensions is critical for survival. While the transcriptional response to acute hypoxia has been well-studied, the post-translational effects of hypoxia and hyperoxia have been underexplored. In this study, we systematically investigate protein turnover rates in mouse heart, lung, and brain under different inhaled oxygen tensions. We find that the lung proteome is the most responsive to changes in oxygen tension, likely due to the direct exposure of alveoli to inhaled oxygen. In particular, several extracellular matrix (ECM) proteins such as collagens and laminins, are stabilized in the lung under both hypoxia and hyperoxia, suggesting their post-translational regulation. Furthermore, we validate our previous finding that complex 1 of the electron transport chain (ETC) is destabilized in hyperoxia, explaining the exacerbation of associated disease models by hyperoxia and rescue by hypoxia. Moreover, we nominate MYBBP1A as a novel transcriptional regulator in hyperoxic lung, particularly in the context of rRNA homeostasis. Overall, our study highlights the importance of the effects of oxygen tensions on protein turnover rates and identifies novel tissue-specific mediators of oxygen-dependent responses.

2023-06-04 | MSV000092095 | MassIVE

Small Extracellular Vesicles from Hypoxic Triple-Negative Breast Cancer Cells induce Oxygen-dependent Cell Invasion

Project description:Hypoxia, a condition of low oxygenation frequently found in triple-negative breast tumors, is often related to increased extracellular vesicle (EV) secretion and favors cell invasion, which is a crucial step for metastasis. Cell invasion is a complex process in which cell morphology is altered due to F-actin cytoskeleton polarization and the establishment of dynamic focal adhesion spots, which coupled with ECM remodeling enables cells to migrate through tissues seeking a new developmental niche. In our in-depth investigation over the invasive properties triggered by TNBC-derived hypoxic small EVs (SEVh) in vitro, we analyzed the morphological, phenotypical and proteomic distinctions promoted by hypoxia and/or SEVh signaling in TNBC cells. SEVh was fully characterized and showed a distinct proteome and abundance profile from its normoxic counterparts. SEVh promotes invasive behaviors exclusively in normoxia, including pro-migratory morphology, invadopodia development, ECM degradation and gelatinase secretion, which indicates the importance of SEVh response on hypoxic settings in tumor progression. In hypoxia, SEVh was responsible for proteolytic and catabolic pathway inducement, interfering with integrin availability and gelatinase expression. Protein profiling of SEVh-treated, normoxic cells indicate a baseline favoring of metabolic processes and cell cycle, modulating cell health away from apoptotic pathways that are enriched in hypoxia. Overall, our results demonstrate the importance of hypoxic signaling via SEV in a tumoral setting for the early establishment of metastasis.

2022-11-01 | PXD035244 | Pride

miRNA profile of Neonatal Rat Cardiomyocytes treated with 0.5% or 1.5% Oxygen for 48 h versus Normoxia

Project description:The Purpose of this study is to screen for microRNAs regulated by hypoxia in neonatal rat cardiomyocytes. 3 biological replicates were perfomed for each each group, normoxia and hypoxia. One normoxic and one hypoxic sample was hybridized to each chip for a total of 6 2-color experiments. A dye swap for each oxygen treatment were performed.

2010-10-28 | E-GEOD-24954 | biostudies-arrayexpress

Hypoxia-responsive gene expression profile of U87 MG glioblastoma cells and their exosomes.

Project description:How cancer cells adapt to hypoxia during tumor development remains an important question. The hypothesis tested in the present study was that tumor cell-derived exosome vesicles (also known as microvesicles or extracellular vesicles) are mediators of hypoxia-dependent intercellular signaling in glioblastoma (GBM), i.e. highly aggressive brain tumors characterized by hypoxia and a vascular density that is among the highest of all human malignancies. In vitro hypoxia experiments and studies with patient materials reveal the enrichment in exosomes of hypoxia-regulated mRNAs and proteins, several of which were associated with poor patient prognosis. We show that cancer cell exosomes mediate hypoxia-dependent, phenotypic modulation of stromal cells in vitro and ex vivo, resulting in accelerated GBM tumor angiogenesis and growth in mice. These data suggest that exosomes constitute potent mediators of hypoxia-driven tumor development, and circulating multiparameter biomarkers of tumor hypoxia. U87 MG glioblastoma cells were grown at normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 48 hours. Conditioned media from normoxic and hypoxic cells were then used to isolate exosomes by differential centrifugation. Both cells and exosomes were lysed in Trizol reagent, and RNA was isolated.Total RNA from all samples (four types of samples in three biological repilicates) was subjected to genome-wide transcriptional analysis with Illumina HumanHT-12 V3.0 expression beadchip. Gene expression profile obtained from hypoxic U87 MG glioblastoma cells was compared to the profile of normoxic control cells. Analogically, gene expression profile obtained from hypoxic U87 MG cells was compared to the profile of exosomes secreted by normoxic U87 MG cells.

2013-03-20 | E-GEOD-45301 | biostudies-arrayexpress

Gene expression responses to oxygen challenge in a panel of human brain organoids

Project description:Gene expression responses to oxygen challenge in a panel of human brain organoids

| PRJNA1143585 | ENA