Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

52 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole Genome Expression after Hypoxia and Reoxygenation in the Newborn Mouse Lung, Brain and Eye

ABSTRACT: Perinatal asphyxia is detrimental to the newborn baby and the use of supplemental oxygen during resuscitation may worsen the prognosis of these babies. The mechanism behind hyperoxic injury is not fully understood and our aim was to investigate four oxygen therapies following hypoxia and these effects on transcriptional activity. A microarray study was performed on 62 C57BL/6 mice randomized into four hypoxia groups (FiO2 0.08, 120 min) reoxygenated with FiO2 0.21, 0.40, 0.60 and 1.0 (30 min), and into two normoxia groups (FiO2 0.21,120 min) reoxygenated with FiO2 0.21 or 1.0, which served as control groups. A 150 min observation time in normoxia followed before animal sacrificing and lung, brain and eye tissue were stored in RNA Later before the microarray analysis were performed.

ORGANISM(S): Mus musculus

SUBMITTER: Ståle Nygård

PROVIDER: E-GEOD-32500 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Combined intermittent and sustained hypoxia is a novel and deleterious cardio-metabolic phenotype

Project description:Study objectives: Chronic obstructive pulmonary disease and obstructive sleep apnea overlap syndrome is associated with excess mortality, and outcomes are related to the degree of hypoxemia. People at high altitude are susceptible to periodic breathing, and hypoxia at altitude is associated with cardio-metabolic dysfunction. Hypoxemia in these scenarios may be described as superimposed sustained plus intermittent hypoxia, or overlap hypoxia (OH), the effects of which have not been investigated. We aimed to characterize the cardio-metabolic consequences of OH in mice. Methods: C57BL/6J mice were subjected to either sustained hypoxia (SH, FiO2=0.10), intermittent hypoxia (IH, FiO2=0.21 for 12 hours, and FiO2 oscillating between 0.21 and 0.06, 60 times/hour, for 12 hours), OH (FiO2=0.13 for 12 hours, and FiO2 oscillating between 0.13 and 0.06, 60 times/hour, for 12 hours), or room air (RA), n=8/group. Blood pressure and intraperitoneal glucose tolerance test were measured serially, and right ventricular systolic pressure (RVSP) was assessed. Results: Systolic blood pressure transiently increased in IH and OH relative to SH and RA. RVSP did not increase in IH, but increased in SH and OH by 52% (p<0.001) and 20% (p=0.001). Glucose disposal worsened in IH and improved in SH, with no change in OH. Serum LDL and VLDL increased in OH and SH, but not in IH. Hepatic oxidative stress increased in all hypoxic groups, with the highest increase in OH. Conclusions: Overlap hypoxia may represent a unique and deleterious cardio-metabolic stimulus, causing systemic and pulmonary hypertension, and without protective metabolic effects characteristic of sustained hypoxia.

2021-12-01 | GSE189958 | GEO

RNA sequencing data for hypoxic and normoxic vessels

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of mouse pulmonary arteries (main, right and left extralobar branches) from C57BL/6 mice exposed to 6 weeks or hypoxia (FiO2 10%) and normoxia (FiO2%)

2021-08-25 | GSE182564 | GEO

Transcriptomics Responses to Hypoxia and Ketamine in Ovine Fetal Cerebral Cortex

Project description:Transient hypoxia in pregnancy stimulates a physiological reflex response that redistributes blood flow and defends oxygen delivery to the fetal brain. The chemoreceptor reflex that is responsible for this physiological response is dependent on glutamatergic neurotransmission which, in times of vigorous activity, could produce cell death secondary to calcium uptake. We designed the present experiment to test the hypotheses that transient hypoxia produces damage of the cerebral cortex and that ketamine, an antagonist of NMDA receptors, reduces the damage. Late-gestation, chronically catheterized fetal sheep were subjected to a 30 min period of ventilatory hypoxia that decreased fetal PaO2 from 17Â±1 to 10Â±1 mm Hg, or normoxia (PaO2 17Â±1 mm Hg), with or without pretreatment (10 min before hypoxia/normoxia) with ketamine (3 mg/kg, iv). One day (24 h) after hypoxia/normoxia, fetal cerebral cortex was removed and mRNA extracted for transcriptomics and systems biology analysis. Hypoxia stimulated a transcriptomics response consistent with a reduction in cellular metabolism and an increase in inflammation. Ketamine pretreatment reduced both of these responses. The inflammation response modeled with transcriptomic system biology was validated by immunohistochemistry and showed increased abundance of microglia/macrophages after hypoxia in the cerebral cortical tissue that ketamine significantly reduced. We conclude that transient hypoxia produces inflammation of the fetal cerebral cortex and that ketamine, in a standard clinical dose, reduces the inflammation response. 4 groups: hypoxia, hypoxia plus ketamine, normoxia, normoxia plus ketamine. Hypoxia produced by low PO2 in maternal inspired gas for 30 min, followed by normoxia recovery for 23.5 hours. Control fetuses maintained at normoxia for 30 min, followed by another 23.5 h of normoxia. Fetal frontal cerebral cortex collected for mRNA at end of 23.5 h recovery period.

2016-04-06 | E-GEOD-76110 | biostudies-arrayexpress

TempO-Seq of human breast cancer MCF-7 and HCC1143 cell lines under acute normoxia and hypoxia

Project description:Comparison of luminal and basal breast cancer cells under acute normoxia and hypoxia. Cells were plated in 96-well plates and incubated 24 hrs under normoxia or hypoxia after which the wells were washed once with cold PBS and lysed using TempO-Seq lysis buffer for 15 min at room temperature. Samples were stored at −80 °C before shipping to BioClavis for whole genome TempO-Seq analysis. For normoxia (NX) 21% oxygen was used and for hypoxia (HX) 1%oxygen was used. Each condition has 3 biological replicates.

2023-06-01 | E-MTAB-12234 | biostudies-arrayexpress

TempO-Seq of human breast cancer MCF-7 and HCC1143 cell lines under chronic normoxia and hypoxia

Project description:Comparison of luminal and basal breast cancer cells under chronic normoxia and hypoxia. Cells were plated in 96-well plates and incubated 5 days under normoxia or hypoxia after which the wells were washed once with cold PBS and lysed using TempO-Seq lysis buffer for 15 min at room temperature. Samples were stored at −80 °C before shipping to BioClavis for whole genome TempO-Seq analysis. For normoxia (NX) 21% oxygen was used and for hypoxia (HX) 1%oxygen was used. Each condition has 3 biological replicates.

2023-06-01 | E-MTAB-12233 | biostudies-arrayexpress

RNA-seq of HeLa cells stably overexpressing SRSF6-GFP grown under normoxic and hypoxic conditions

Project description:We used HeLa cells that overexpress GFP-tagged SRSF6 (4-fold) were grown in normal conditions (Normoxia, 21% oxygen) or hypoxic conditions (Hypoxia, 0.2% oxygen). compared the binding pattern of SRSF6 between normoxia, 4h hypoxia and 24h hypoxia.

2023-01-03 | GSE198308 | GEO

The Genomics of the Fetal Hypothalamic Cellular Response to Transient Hypoxia: Endocrine, Immune, and Metabolic Responses

Project description:Fetuses respond to transient hypoxia (a common stressor in utero) with cellular responses that are appropriate for promoting survival of the fetus. The present experiment was performed to identify the acute genomic responses of the fetal hypothalamus to transient hypoxia. Three fetal sheep were exposed to 30 min of hypoxia and hypothalamic mRNA extracted from samples collected 30 min after return to normoxia. These samples were compared to those from 4 normoxic control fetuses using the Agilent 019921 ovine array. Differentially-regulated genes were analyzed by network analysis and by gene ontology analysis, identifying statistically significant overrepresentation of biological processes. Real-time PCR of selected genes supported the validity of the array data. Hypoxia induced increased expression of genes involved in response to oxygen stimulus, RNA splicing, anti-apoptosis, vascular smooth muscle proliferation, and positive regulation of Notch receptor target. Downregulated genes were involved in metabolism, antigen receptor-mediated immunity, macromolecular complex assembly, S-phase, translation elongation, RNA splicing, protein transport, and post-transcriptional regulation. We conclude that these results emphasize that the cellular response to hypoxia involves reduced metabolism, the involvement of the fetal immune system, and the importance of glucocorticoid signaling. 3 Ventilatory Hypoxia (VH) and 4 Control (con) fetuses. All fetuses were chronically catheterized and in late gestation. Hypoxia produced by low PO2 in maternal inspired gas for 30 min, followed by normoxia recovery for 30 min. Control fetuses maintained at normoxia for 30 min, followed by another 30 min of normoxia. Hypothalami collected for mRNA at end of normoxic recovery period.

2014-01-16 | E-GEOD-43371 | biostudies-arrayexpress

Effect of graded normobaric hypoxia on Genome-wide expression in healthy individuals

Project description:The regulation of oxygen homeostasis is critical in physiology and disease pathogenesis. Studying transcriptomic profiles after hypoxia exposure could potentially uncover valuable biomarkers for predicting responses. To this end, 6 healthy individuals were recruited and exposed to graded normobaric hypoxia (FiO2 ~ 0.19 up till 0.13 in steps of 2% decrement in 10 minutes). A blood sample was collected before (at room air) and after the graded normobaric hypoxia exposure (at FiO2 ~ 0.13) for the gene-expression profiles. Results provide important information about early molecular differences induced by our experimental protocol in young, healthy individuals.

2024-12-30 | GSE265882 | GEO

The effects of mild intermittent hypoxia exposure on the abdominal subcutaneous adipose tissue proteome in overweight and obese men: A first-in-human randomized, single-blind, cross-over study

Project description:Adipose tissue (AT) oxygen tension (pO2) has been implicated in AT dysfunction and metabolic perturbations in both rodents and humans. Compelling evidence suggests that hypoxia exposure alters metabolism, at least partly through effects on AT. However, it remains to be elucidated whether mild intermittent hypoxia (MIH) exposure impacts the AT proteome. We performed a randomized, single-blind, cross-over study to investigate the effects of seven consecutive days of MIH (FiO2 15%, 3x2h/d) compared to normoxia (FiO2 21%) exposure, on the AT proteome in overweight/obese men. AT insulin sensitivity was determined by a two-step hyperinsulinemic-euglycemic clamp, and abdominal subcutaneous AT biopsies were collected (n=11) under normoxic, fasting conditions following both exposure regimens. AT proteins were isolated and quantified using liquid chromatography-mass spectrometry. After correction for blood contamination, 1022 AT protein IDs were identified, of which 123 were differentially expressed following MIH (p < 0.05). These proteins were involved in redox systems, cell-adhesion, actin cytoskeleton organization, extracellular matrix composition and energy metabolism. We demonstrate for the first time that MIH exposure impacts the AT proteome. Moreover, differential AT TMOD3 expression is related to changes in AT insulin sensitivity, thereby linking MIH-induced effects on the AT proteome to metabolic changes in overweight/obese humans.

2022-02-16 | PXD029213 | Pride

Profile of mRNAs associated with Ago (Argonaute) 1 in normoxic and hypoxic endothelial cells

Project description:Messenger RNAs that are bound to Ago1 is to be transcriptionally or translational suppressed. Therefore the changes in Ago1-associated transcripts indicate the changes of suppression of these genes. We used microarrays to detail changes of mRNA transcripts that are associated with Ago1 in endothelial cells under normoxia and hypoxia conditions. Human umbilical vein endothelial cells pooled from 8 different sources were subjected to normoxia (21% oxygen, Nx) or hypoxia (2% hypoxia, Hx) for 24 hr. Ago1 was immunoprecipitated with mouse anti-human Ago1 using a lysis buffer containing 0.1% NP-40. The associated RNA was extracted and hybridized on Affymetrix Human Gene 1.0 ST arrays.

2013-06-30 | E-GEOD-43165 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data