Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clock genes in human oral mucosa

ABSTRACT: Circadian rhythms are daily oscillations of multiple biological processes driven by endogenous clocks. Imbalance of these rhythms has been associated with cancerogenesis in humans. To further elucidate the role of the circadian clock in cellular growth control, tumor suppression and cancer treatment, a standard of circadian gene regulations in healthy men is essential. Comparative microarray analyses were conducted investigating the relative mRNA expression of clock genes throughout a 24-hour period in biopsies obtained from oral mucosa of eight healthy diurnally active male study participants. A custom-designed oligo-based microarray which in addition to oncogenes and inflammatory genes contains probes for 20 clock genes and 70 clock-associated genes in human was used. Keywords: Human gene expression study Reference design with Cy3 labeled uniRNA and Cy5 labeled sample RNA.

ORGANISM(S): Homo sapiens

SUBMITTER: Kay Nieselt

PROVIDER: E-GEOD-11469 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Mesenchymal stem cell labelings with ferritin

Project description:Mesenchymal stem cells (MSC) omplexed to different transfection agents (R60, R200, DOSPER, jetPei, Pulsin). Two MSC populations (h21 and h24) and two passages (P2 and P4) were tested with different labelings. In a direct design experiment each sample was compared to its unlabeled control sample. Keywords: Human gene expression study Reference design with unlabeled cells in the Cy3 reference channel, and labeled cells in the Cy5 channel.

2010-05-16 | E-GEOD-11470 | biostudies-arrayexpress

Lactate modulates gene expression in human mesenchymal stem cells

Project description:Wound healing is associated with high rates of cell replication and lactate accumulation even under normoxic and hyperoxic conditions. Lactate accounts for various effects in tissue regeneration, such as collagen synthesis, angiogenesis, modulation of cytokine patterns and as recently shown for stem cell homing. Its influence on genes involved in cell replication has not been shown yet. Therefore, the effect of lactate considering genes involved in different cellular processes was investigated. Human umbilical vein endothelial cells (HUVEC) were cultured and incubated with lactate for different periods of time. Gene expression analysis was performed using custom-designed oligonucleotide microarrays. Keywords: Human gene expression study Reference design with Cy3 labeled uniRNA and Cy5 labeled sample RNA.

2010-05-15 | E-GEOD-11458 | biostudies-arrayexpress

Downregulation of three tumour suppressor genes SLC26A3, DCN and TPM1 in colorectal cancer

Project description:Despite identification of major genes and pathways involved in development of colorectal cancer (CRC) it became obvious that several steps in these pathways might be bypassed by other yet unknown genetic events that lead towards CRC. To improve our understanding of the genetic mechanisms of CRC development we used microarrays to identify novel genes involved in development of CRC. In order to identify possible novel genes involved in the development of colorectal cancer we analysed the expression profile of 16 colorectal cancers. We used dual color approach. Tumour tissue was labeled with Cy5 and corresponding normal tissue was labeled with Cy3. Each array contained at least 4 replicate spots for each gene analysed. Expression was obtained by calculating median from replicate spots. Genes not present in at least 100% of all samples were filtered out. Median value for each gene from 16 arrays was calculated.

2010-06-20 | E-GEOD-14010 | biostudies-arrayexpress

Salmonella Typhiumurium LT2, wild type versus rfaC mutant.

Project description:Transcriptional analysis of rfaC mutant strain compared to an isogenic wild type strain Salmonella Typhimurium. Keywords: Genetic modification. Three independent biological replicates.

2010-05-15 | E-GEOD-19878 | biostudies-arrayexpress

Salmonella Typhiumurium LT2, wild type versus aroD mutant.

Project description:Transcriptional analysis of aroD mutant strain compared to an isogenic wild type strain Salmonella Typhimurium. Keywords: Genetic modification. Three independent biological replicates.

2010-05-25 | E-GEOD-9411 | biostudies-arrayexpress

Comparative genomic hybridization of wild type yeast isolated from clinical samples and wine fermentations to investigate genetic variability in yeast from different ecological niches

Project description:Using microarrays targeting the complete ORFeome of Saccharomyces cerevisiae S288c, this study investigates the genetic variability present in wild type yeast from different ecological niches by comparative genome hybridization on array (aCGH). Genomic DNA of Saccharomyces strains isolated from clinical samples and strains from wine fermentations, either commercially available or isolated form spontaneous wine fermentations, was compared to genomic DNA of the sequenced laboratory strain S288c, using a common reference experimental design, with two dye-swap replicate hybridizations for each strain and six S288c self-self hybridizations for background noise estimation, in a total of 38 hybridizations.

2008-10-01 | E-MTAB-29 | biostudies-arrayexpress

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection

Project description:This SuperSeries is composed of the following subset Series: GSE15746: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1 GSE15747: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2 Refer to individual Series

2010-05-19 | E-GEOD-15801 | biostudies-arrayexpress

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2

Project description:Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species. We have developed a method to profile genome wide methylation. 7 ovarian normal samples and 11 tumor samples from other individuals were analyzed for CpG methylation. After inter array normalization, the tumor samples were taken together and the methylation compared to that of the normal samples to identify regions of the CpG islands that are significantly altered between the two datasets. Some of these regions were validated for their methylation as a proof of principle for the method.

2010-05-19 | E-GEOD-15747 | biostudies-arrayexpress

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1

Project description:Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species. We have developed a method to profile genome wide methylation. 12 breast normal samples and matching tumors from these individuals and an additional 28 tumor samples from other individuals were analyzed for CpG methylation. After inter array normalization, the tumor samples were taken together and the methylation compared to that of the normal samples to identify regions of the CpG islands that are significantly altered between the two datasets. Some of these regions were validated for their methylation as a proof of principle for the method.

2009-04-28 | E-GEOD-15746 | biostudies-arrayexpress

Transcription profiling of mouse 3T3-L1 adipocyte differentiation time series-3T3-L1 adipocyte differentiation timeseries

Project description:3T3-L1 adipocyte differentiation time series-3T3-L1 adipocyte differentiation timeseries. Hackl H*, Burkard T*, Sturn A, Rubio R, Schleiffer A, Tian S, Quackenbush J, Eisenhaber F, Trajanoski Z. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol. 2005. 6:R108.

2005-01-01 | E-MARS-2 | 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