In vitro and in vivo analysis of hypoxic gene expression in rat gliomas
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE25980 | GEO | 2011/01/13
SECONDARY ACCESSION(S): PRJNA135523
REPOSITORIES: GEO
Similar Datasets
Project description:In vivo profiling of hypoxic gene expression in gliomas using the hypoxia marker EF5 and laser-capture microdissection We have employed the hypoxia marker EF5 coupled with laser capture microdissection to isolate RNA from viable hypoxic and normoxic regions of 9L experimental gliomas. We report the identification of the hypoxic gene expression profile in a solid tumor using a prototypical hypoxia marker EF5, Laser Capture Microdissection (LCM) and Microarray Gene Expression Profiling (EF5-LCM-MGEP). We have utilized LCM to isolate total RNA from normoxic and hypoxic regions in the rat 9L glioma tumor model grown in its isogenic host (Fischer rat). Microarray analysis of the isolated RNA generated an in vivo hypoxia expression profile. For comparison, we also analyzed RNA samples isolated from rat 9L glioma cells in culture exposed to hypoxia or normoxia.
2011-01-13 | E-GEOD-25980 | biostudies-arrayexpress
Project description:Genome wide analysis RNA polymerase II (RNA Pol II) and histone marker H3K4me3 in hypoxia and normoxia using ChIP-seq. Breast cancer cell line (MCF-7) is cultured in normoxic condition (21% O2) and hypoxic condition (0.5%O2) for 16 hours. Immunoprecipitation of RNA Pol II and H3K4me3.
2014-02-10 | E-MTAB-1995 | biostudies-arrayexpress
Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression. Two-condition experiment, Normoxic MSCs vs. Hypoxic MSCs.
2011-02-19 | E-GEOD-20463 | biostudies-arrayexpress
Project description:Microarray of whole blood maternal samples comparing the expression of genes in the maternal blood in pregnancies where the fetus was hypoxic at birth compared to those where the fetus was normoxic at birth. Intrapartum hypoxia is associated with severe neonatal morbidity and mortality. Current techniques to assess fetal hypoxic status during labour have a poor sensitivity. At birth, the lactate level in umbilical cord blood is used to assess the degree of fetal hypoxia during birth, such that a high lactate reflects a hypoxic fetus and a low lactate a normoxic fetus. We collected maternal blood prior to delivery and compared the expression of genes in the maternal blood in women delivering a normoxic or hypoxic fetus as evidenced by umbilcal cord blood levels.
2014-05-08 | E-MTAB-2054 | biostudies-arrayexpress
Project description:Laser capture microdissection was used to obtain individual LGN layers for DNA microarray of Rhesus array in macaque monkeys that Monocular Visual Deprivation was generated by either opaque dark contact lens or tarsoraphoplasty at birth. Keywords: Lateral Geniculate Nucleus, monocular deprivation, Rhesus array, Laser Capture Microdissection, Gene expression
2008-12-01 | GSE9795 | GEO
Project description:Laser capture microdissection (LCM) provides a useful method for isolating specific cells or tissues from biological samples. Here, we adapted microdissection protocols to allow high-resolution transcript analysis of different tissues from developing Arabidopsis seed. However, to obtain enough RNA for microarray analyses it was necessary to amplify the RNA. Microarray analyses, using endosperm derived RNA amplified by two-round IVT, reproducibly identified endosperm enriched marker genes. Keywords: LCM Endosperm Arabidopsis
2007-04-02 | GSE6663 | GEO
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
Project description:Cornerstones of the regulatory phenomena observed in hypoxic HPV-positive cancer cells are: (i) hypoxia blocks E6/E7, an effect that can be counteracted by (ii) AKT inhibition and by (iii) high glucose supply. To gain further insights into the underlying regulatory circuits, mass spectrometry-based quantitative proteome analyses were performed comparing normoxic and hypoxic SiHa cells and assessing their response towards AKTi VIII and 25 mM glucose under hypoxia
2019-02-18 | PXD011095 | Pride
Project description:Hypoxia triggers aggressive cancer growth and contributes to chemotherapy resistance. Novel therapeutic strategies aim at targeting hypoxia activated signaling pathways. Tumor hypoxia not only affects neoplastic tumor cells but also the surrounding stroma cells. Therefore, a novel ex vivo model was established, which allows the study of hypoxia effects in fragments of non-small cell lung cancer (NSCLC) with preserved tumor microenvironment and 3D-structure. Microarray analysis identified 107 significantly regulated genes with at least two-fold expression change in hypoxic compared to normoxic fragments. However, only four genes were significantly regulated in both subtypes, adenocarcinoma and squamous cell carcinoma. The hypoxic regulation of these four genes was verified in an independent set using quantitative PCR. Non-small cell lung cancer (NSCLC) fragments were cultured ex vivo under hypoxia or normoxia for three days. cDNA microarray analysis was performed in hypoxic and normoxic lung cancer fragments from ten patients.
2011-07-27 | E-GEOD-30979 | biostudies-arrayexpress
Project description:Transcriptional profiling of H1299 non-small cell lung carcinoma cells transfected with either wt p53 or mut(175) p53 driven by the 5xHRE promoter (5 repeats of hypoxia-inducible factor response elements) and treated for 16 h with normoxia (21% O2) or hypoxia(<0.1% O2). 5xHRE promoter ensures that p53 expression is induced in hypoxic conditions only. Goal was to determine the transcriptional response of p53 in hypoxia and the 175 p53 mutant was used as a control as it is DNA-binding defective and transcription-incompetent mutant. Four-condition experiment: wt p53-transfected H1299 cells treated with normoxia, mut p53-transfected H1299 cells treated with normoxia, wt p53-transfected H1299 cells treated with hypoxia, mut p53-transfected H1299 cells treated with hypoxia. Biological replicates: 1 normoxic sample with wt p53, 1 normoxic sample with mut p53, 3 hypoxic samples with wt p53, 3 hypoxic samples with mut p53.
2014-01-08 | E-GEOD-53893 | biostudies-arrayexpress