Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from mouse B16-F10 cells exposed to hypoxic conditions in vitro.

ABSTRACT: Analysis of gene expression profile of B16-F10 murine melanoma cells exposed to hypoxic conditions (1% oxygen) or hypoxia mimicry (cobalt chloride) for 24 hours. Gene expression profiles were analyzed using MG-U74Av2 oligonucleotide microarrays. Data analysis revealed 2541 probesets (FDR<5%) for 1% oxygen experiment and 364 probesets (FDR<5%) for cobalt chloride, that showed differences in expression levels. Analysis of hypoxia-regulated genes (1% O2) by stringent Family-Wise Error Rate estimation indicated 454 significantly changed transcripts (p<0.05). The most upregulated genes were Lgals3, Selenbp1, Nppb (more than ten-fold increase). Both hypoxia and hypoxia-mimicry induced HIF-1 regulated genes. However, unsupervised analysis (Singular Value Decomposition) revealed distinct differences between gene expression induced by these two experimental conditions.

ORGANISM(S): Mus musculus

PROVIDER: GSE33607 | GEO | 2011/11/11

SECONDARY ACCESSION(S): PRJNA148531

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from mouse B16-F10 cells exposed to hypoxic conditions in vitro.

Project description:Analysis of gene expression profile of B16-F10 murine melanoma cells exposed to hypoxic conditions (1% oxygen) or hypoxia mimicry (cobalt chloride) for 24 hours. Gene expression profiles were analyzed using MG-U74Av2 oligonucleotide microarrays. Data analysis revealed 2541 probesets (FDR<5%) for 1% oxygen experiment and 364 probesets (FDR<5%) for cobalt chloride, that showed differences in expression levels. Analysis of hypoxia-regulated genes (1% O2) by stringent Family-Wise Error Rate estimation indicated 454 significantly changed transcripts (p<0.05). The most upregulated genes were Lgals3, Selenbp1, Nppb (more than ten-fold increase). Both hypoxia and hypoxia-mimicry induced HIF-1 regulated genes. However, unsupervised analysis (Singular Value Decomposition) revealed distinct differences between gene expression induced by these two experimental conditions. We investigated transcriptional activity of B16-F10 murine melanoma cells cultured for 24h under hypoxic (nominal 1% oxygen; 9 experimental samples and 6 controls) and hypoxia-mimicking conditions (cobalt chloride, 100 M-NM-<M or 200 M-NM-<M, 2 samples each and 2 controls).

2011-11-11 | E-GEOD-33607 | biostudies-arrayexpress

Hypoxia and Hypoxia mimics

Project description:Comparison between hypoxia (1%O2) and cobalt chloride (100 uM) and deferoxamine (100 uM) and Nickel Chloride (100 uM) in Hep3B cells (human hepatocellular carcinoma cells) Keywords = Hep3B Keywords = hypoxia Keywords = cobalt Keywords = deferoxamine Keywords = Nickel Keywords: ordered

2004-02-27 | GSE1056 | GEO

Transcription profiling of Hep3B cells response hypoxia (1%O2) and cobalt chloride (100 uM) and deferoxamine (100 uM) and Nickel Chloride (100 uM)

Project description:Comparison between hypoxia (1%O2) and cobalt chloride (100 uM) and deferoxamine (100 uM) and Nickel Chloride (100 uM) in Hep3B cells (human hepatocellular carcinoma cells)

2008-06-12 | E-GEOD-1056 | biostudies-arrayexpress

ChIP-seq of H3K27acethylation of human aortic endothelial cells (HAECs) treated with Cobalt chloride (CoCl2)

Project description:Endothelial-to-mesenchymal transition (EndMT) is a fundamental process in vascular remodeling, and hypoxia is known to induce EndMT and involved in cardiovascular disease development. Cobalt chloride (CoCl2), a chemical inducer of hypoxia-inducible factor-1 (HIF-1) could influence cellular function and its differentiation. However, exact molecular mechanism how stabilization of HIF-1 by cobalt chloride in human primary ECs affects cellular behavior and EndMT process is largely unknown. In this study, we performed ChIP-seq for H3K27ac in human aortic endothelial cells (HAECs) treated with CoCl2

2021-11-18 | GSE189071 | GEO

Integrated mRNA/miRNA-seq of Caco-2 and HT-29 cells under chemical hypoxia (cobalt chloride, oxyquinoline)

Project description:To uncover hypoxia-induced miRNA-mRNA interactions landscape in colorectal cancer cell lines we performed integrated miRNA/mRNA sequencing of Caco-2 and HT-29 cells. Hypoxia was chemically induced via 24 h cobalt(II) chloride and oxyquinoline treatments.

2020-09-29 | GSE158632 | GEO

Gene and exon expression of Human Umbilical Vein Endothelial Cell under Mimic Hypoxia Stress

Project description:Human umbilical vein endothelial cells (HUVECs) were insulted with cobalt chloride to induce cell apoptosis and alternative splicing in the mimic-hypoxia environment. We use Affymetrix exon array to reveal differential expression from transcript-level and exon-level in genome-wide.

2009-04-01 | GSE12546 | GEO

Metabolic reprogramming of Kaposi’s sarcoma associated herpes virus infected B-cells in hypoxia

Project description:We report differential gene expression in BJAB-KSHV/BJAB cells treated with Cobalt chloride/BJAB-KSHV cells treated with Cobalt Chloride compared to BJAB cells

2018-05-19 | GSE114625 | GEO

Biogenerated oxygen-related environmental stressed apoptotic body targets endothelial cells

Project description:he dynamic balance of hypoxia and oxidative stress constitutes the oxygen-related microenvironment in injured tissues. Oxygen homeostasis is highly variable; therefore, it is not a therapeutic target for injured tissue repair. We found an enrichment and extensive apoptosis of mesenchymal stem cells (MSCs) infused intravenously in the wound microenvironment with co-existing hypoxia and oxidative stress. Apoptotic bodies (ABs), generated from in situ apoptosis, significantly promotes angiogenesis. We improved the derivation pathway of ABs by simulating oxygen homeostasis in injured tissues, with cobalt chloride-induced hypoxia or hydrogen peroxide-induced oxidative stress in MSCs. Oxygen-related environmental stressed ABs, derived from environments of hypoxic and oxidative stress, were identified and loaded onto hydrogel microspheres for accurate regulation of endothelial cells (ECs) vascularization. These ABs directly targeted ECs; oxidative stress ABs (Oxi-ABs) have a 2.5- and 4-fold higher tube-forming ability than hypoxic and normoxic ABs, respectively. miRNA microarray analysis revealed that different oxygen-stressed ABs deliver similar miRNAs, which leads to the broad upregulation of EC phosphokinase activity. Finally, local delivery of Oxi-ABs-loaded hydrogel microspheres promotes wound healing. Oxi-ABs-loaded hydrogel microspheres achieved controlled AB release, targeting EC by reducing the consumption of early inflammatory cells and adapting to the proliferative phase of wound healing. Thus, the biogenerated apoptotic bodies responding to oxygen-related environmental stress can target ECs to promote vascularization.

2024-01-01 | GSE240216 | GEO

Identifying pH independent hypoxia induced genes in human squamous cell carcinomas in vitro

Project description:Background: Genes upregulated by low oxygen have been suggested as endogenous markers for tumor hypoxia. Yet, most of the genes investigated have shown inconsistent results, which have led to concerns about their ability to be true hypoxia markers. Previous studies have demonstrated that expression of hypoxia induced genes can be affected by extracellular pH (pH e ). Methods: Five different human cell lines (SiHa, FaDu DD, UTSCC5, UTSCC14 and UTSCC15) were exposed to different oxygen concentrations and pH (7.5 or 6.3), and gene expression analyzed with microarray (Affymetrix - Human Genome U133 Plus 2.0 Array). Results: An analysis of two of the cell lines using SAM identified 461 probesets that were able to separate the four groups “ Normal oxygen, normal pH ” , “ Low oxygen, normal pH ” , “ Normal oxygen, low pH ” and “ Low oxygen, low pH ” . From here it was possible to identify a fraction of probesets induced at low oxygen independent of pH in these two cell lines, this fraction included HIG2, NDRG1, PAI1 and RORA. Further verifi cation by qPCR highlighted the necessity of using more cell lines to obtain a robust gene expression profi les. To specifi cally select pH independent hypoxia regulated genes across more cell lines, data for FaDu DD, UTSCC5, UTSCC14 and UTSCC15 were analyzed to identify genes that were induced by hypoxia in each cell line, where the induction was not affected by low pH, and where the gene was not signifi cantly induced by low pH alone. Each cell line had 65 – 122 probesets meeting these criteria. For genes to be considered as target genes (hypoxia inducible pH independent), genes had to be present in three of four cell lines. Conclusion: The result is a robust hypoxia profile unaffected by pH across cell lines consisting of 27 genes. This study demonstrates a way to identify hypoxia markers by microarray, where other factors in the tumor microenvironment are taken into account.

2015-06-20 | GSE70051 | GEO

Zebrafish fins: normoxic Controls vs. hypoxic fins

Project description:Transcriptional profiling of zebrafish fins comparing control fins and hypoxic fins (cobalt chloride (CoCl2, 1 mM)

2017-02-09 | GSE58568 | GEO