Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA88003 | ENA |
REPOSITORIES: ENA
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Project description:Identification of genes in DNA damage response and repair pathways differentially transcribed or translated under anoxia or hypoxia in GM05757 normal human fibroblast cells and DU145 human prostate cancer cells. Comparison of mRNA abundance and translation efficiency of genes in DNA damage response and repair pathways in selected anoxia/hypoxia-treated cells with those in normoxia-treated controls.
2015-07-01 | E-GEOD-52461 | biostudies-arrayexpress
Project description:Cells were grown in light (R0K0) SILAC media (AthenaES) for 7 days, they were then incubated in light media for 24 hours in respective condition (normoxia neutral (NN) pH: 7.4; hypoxia neutral (HN)1% O2, pH: 7.4; hypoxia acidosis (HA), 1% O2, pH=6) and pulsed with heavy (R10K8) SILAC media (AthenaES) for 16 hr (TMT-pSILAC) following treatment.
2020-09-28 | PXD015643 | Pride
Project description:The environment inside even a small tumor is characterized by total (anoxia) or partial oxygen deprivation, hypoxia. It has been shown that radiotherapy and some conventional chemotherapies may be less effective in hypoxia, and therefore it is important to investigate how different drugs act in different microenvironments. In the associated study we performed a large screening of the effects of 19 clinically used or experimental chemotherapeutic drugs on four different cell lines in conditions of normoxia, hypoxia and anoxia. A panel of 19 commercially available drugs: 5-fluorouracil, acriflavine, bortezomib, cisplatin, digitoxin, digoxin, docetaxel, doxorubicin, etoposide, gemcitabine, irinotecan, melphalan, mitomycin c, rapamycin, sorafenib, thalidomide, tirapazamine, topotecan and vincristine were tested for cytotoxic activity on the cancer cell lines A2780 (ovarian), ACHN (renal), MCF-7 (breast), H69 (SCLC) and U-937 (lymphoma). Parallel aliquots of the cells were grown at different oxygen pressures and after 72 hours of drug exposure viability was measured with the fluorometric microculture cytotoxicity assay (FMCA). Sorafenib, irinotecan and docetaxel were in general more effective in an oxygenated environment, while cisplatin, mitomycin c and tirapazamine were more effective in a low oxygen environment. Surprisingly, hypoxia in H69 and MCF-7 cells mostly rendered higher drug sensitivity. In contrast ACHN appeared more sensitive to hypoxia, giving slower proliferating cells, and consequently, was more resistant to most drugs. Gene expression analysis was performed on MCF-7 cells after 90 hours in either anoxic or hypoxic conditions, and compared to cells grown in a regular cell incubator. The gene expression analysis was performed to validate that the cells were hypoxic/anoxic and showed the characteristic hypoxia response. Microarray based mRNA profiling was used to charactarize cells grown in hypoxia and anoxia. In the associated study we performed a large screening of the effects of 19 clinically used or experimental chemotherapeutic drugs on four different cell lines in conditions of normoxia, hypoxia and anoxia. We fin that hypoxia/anoxia render cancer cells both more resistant and more sensistive, depending of the type of drug used. The gene expression analysis was performed to validate that the cells really were hypoxic/anoxic and showed the characteristic hypoxia response. The cell line used for the gene expression analysis was MCF-7.
2014-05-04 | E-GEOD-47009 | biostudies-arrayexpress
Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, RPMI8226-HR derived from RPMI8226 cells, KMS-11-HR derived from KMS-11, U266-HR derived from U266, and IM-9-HR derived from IM-9 cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used RPMI8226 cells and RPMI8226-HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells (normoxia or hypoxia) and exosomes derived from RPMI8226-HR cells (hypoxia-resistant, HR sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the RPMI8226-HR cells significantly increased tube formation of HUVECs than those from RPMI8226 cells.
2018-02-06 | GSE110113 | GEO
Project description:Neutrophils are key effector cells of the innate immune response and are required to migrate and function within highly adverse micro-environmental conditions. These inflammatory sites are characterised by low levels of oxygen. We examined the relative transcript abundance detected in an apoptosis targeted gene array following invitro neutrophil culture (3/6 hrs) in normoxic, hypoxic and anoxic conditions.
2010-06-09 | E-GEOD-968 | biostudies-arrayexpress
Project description:Neutrophils are key effector cells of the innate immune response and are required to migrate and function within highly adverse micro-environmental conditions. These inflammatory sites are characterised by low levels of oxygen. We examined the relative transcript abundance detected in an apoptosis targeted gene array following invitro neutrophil culture (3/6 hrs) in normoxic, hypoxic and anoxic conditions. Keywords: repeat sample
2004-01-17 | GSE968 | GEO
Project description:The rainbow trout, Oncorhynchus mykiss, is relatively sensitive to hypoxia and does not survive deep hypoxia or anoxia. Given this lack of hypoxia-tolerance in the whole animal, the aim of this experiment was to investigate the in vitro responses of cultured rainbow trout cells following anoxia exposure. Rainbow trout hypodermal fibroblast (RTHDF) cells were exposed to anoxia for 12 and 24 h, whilst control cells were held under normoxic conditions for 24 h. Differential gene expression as a consequence of the treatments was analysed using an oligoarray composed of approximately 21,500 BLAST-identified sequences fabricated on the Agilent microarray platform. 57 genes were found to display significant responses to oxygen deprivation and these genes were assigned Gene Ontology terms and IDs. Of the 57 differentially expressed genes, 6 genes associated with carbohydrate metabolism were up-regulated following anoxia, these included phosphoglucomutase (PGM) and glycogen phosphorylase, consistent with glycogen serving as an important energy source during anoxia. Other genes up-regulated in response to anoxia included a number of putative targets of hypoxia inducible factor 1 alpha (HIF1A), namely phosphoglycerate kinase, triosephosphate isomerase and the glucose transporter, GLUT2. Egl9 homolog 3, the proline hydroxylase responsible for HIF1A regulation, was also induced. This analysis indicates that cultured trout cells have the capacity for adaptive gene responses when subjected to oxygen levels that are lethal to the whole organism.
2008-06-11 | E-MAXD-41 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to investigate the role of interplay between circadian clock and oxygen-sensing pathways in determining myogenic progenitor cell fate. Methods: Total RNAs were extracted from wild-type and Bmal1-/- myoblasts following exposure to normoxia (21% O2) or hypoxia (1% O2) for 6 hours, and subjected to RNA-sequencing. Results: There were significantly up-regulated (443 in normoxia versus 477 in hypoxia) and down-regulated (745 in normoxia versus 796 in hypoxia) genes in Bmal1-/- cells compared to wild-type, with a large degree of overlap between hypoxia and normoxia, although the fold change of differential gene expression was generally greater under hypoxia versus normoxia. Conclusion: Loss of Bmal1 in myoblasts leads to a premature differentiation-prone transcriptome, which was exaggerated following exposure to hypoxia.
2022-07-01 | GSE184741 | GEO
Project description:Extracellular vesicles (EVs) represent a diverse group of small membrane-encapsulated particles and provide a universal molecular cell-cell communication system. Hypoxia is a typical condition in solid tumors, and cancer-derived EVs support growth and invasion of tissues by tumor cells. EVs were purified from cell culture medium by ultracentrifugation followed by size exclusion chromatography with Exo-spin™ columns (Cell Guidance Systems Ltd). We performed proteomic analysis of five hypoxia/normoxia pairs of EV samples; each of these replicates for either hypoxia or normoxia was analyzed in duplicates. Obtained data were compared with proteomics analysis of corresponding cell culture media supernatants (SN) after EV removal with 100 000 g ultracentrifugation. We found that exposure of tumor cells to hypoxia (1% oxygen) induced EV secretion, altered EV sizes, and led to notable changes in the EV protein cargo in comparison to normoxia.
2022-02-16 | PXD023546 | Pride