Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA222796 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:UV-C dose and time range finding study on Mouse Embryonic Fibroblasts (MEFs)
| PRJNA219390 | ENA
Project description:In molecular biology, the design of mechanistic experiments has to be optimized by considering statistical and biological principles. In contrast to statistical principles, biological principles of experimental design are not universally formulated. In an attempt to pinpoint generally acceptable rules, we investigated the importance of determining the optimal ranges of scale of i.e. dose and time in gene expression experiments. We propose a protocol for executing small scale, genome wide, range finding studies, covering a wide range of the potentially relevant part of the design space to find the optimal ranges of experimentation. This protocol is executed and a proof-of-concept is presented, where this approach is tested for both an in-vitro and an in-vivo study that aim to unravel DNA repair mechanisms provoked after UV radiation. We identified four challenges of range finding studies in omics experimentation; (1) the modularity of biological processes, (2) their dynamics, (3) the extent to which end-points indicate biological processes, and (4) the costs associated with the assays, which are all addressed by our approach. 57 skin biopt samples taken from 12 individual mice on 8 timepionts and for 6 different UV-B doses. Per mouse 5 skin biopts were samples in time
2014-09-01 | E-GEOD-51348 | biostudies-arrayexpress
Project description:An in-vivo experiment with UV-B exposure of the skin of nude, male mice, with and without human-derived p53 variants in their genome to investigate the cellular responses upon UV-induced DNA damage. Essentially, 4 replicate mice were used for each level of UV-exposure. For each mouse a biopsy of the skin was sampled 5-6 times at different recovery time points after UV-pulse exposure, which resulted in paired samples. In total 132 treated and 132 untreated samples were taken from 64 male mice.
2016-03-01 | GSE63044 | GEO
Project description:Exposure of skin to ultraviolet radiation (UV-R), in the form of both natural and artificial tanning, strongly increases the risk for developing skin cancer. On a molecular level, exposing cells and tissues to UV-R results in well-documented transcriptional changes. However, many of the previous investigations into these transcriptional responses did not adequately characterize the UV emissions or only assessed a limited number of doses or post-exposure times. As a result, our objectives were to provide a mechanistic study that describes the dose- and time-dependent changes in gene expression that drive adverse short-term (e.g. sunburn) and long-term actinic (e.g. skin cancer) possibly delineating response thresholds. In the current study, we examined transcriptomic expression data from mouse skin following exposure to five erythemally-weighted doses (0, 5, 10, 20, 40 mJ/cm2) of UV-R emitted from a UV-emitting tanning device, with six post-exposure durations of 0, 6, 24, 48, 72 and 96 hours (h). Surprisingly, the lowest sub-erythemal dose of 5 mJ/cm2, produced 116 significant DEGs at 96 h post-exposure related to genes associated with structural changes associated with UV-R damage. The largest number of significant changes in gene expression were found at the 6 and 48 h post-exposure time points at the doses of 20 and 40 mJ/cm2. At the highest dose of 40 mJ/cm2, 13 differentially expressed genes of interest were commonly perturbed across all post-exposure time points relative to the time-matched control groups. UV-R exposure induced pathways related to oxidative stress, P53 signaling, inflammation, biotransformation, skin barrier maintenance and innate immunity. The transcriptional data generated in this in vivo study provides mechanistic insight into the short-term and potential long-term health effects of exposure to UV-R tanning that may not be threshold dependent.
2024-10-01 | GSE245747 | GEO
Project description:In molecular biology, the design of mechanistic experiments has to be optimized by considering statistical and biological principles. In contrast to statistical principles, biological principles of experimental design are not universally formulated. In an attempt to pinpoint generally acceptable rules, we investigated the importance of determining the optimal ranges of scale of i.e. dose and time in gene expression experiments. We propose a protocol for executing small scale, genome wide, range finding studies, covering a wide range of the potentially relevant part of the design space to find the optimal ranges of experimentation. This protocol is executed and a proof-of-concept is presented, where this approach is tested for both an in-vitro and an in-vivo study that aim to unravel DNA repair mechanisms provoked after UV radiation. We identified four challenges of range finding studies in omics experimentation; (1) the modularity of biological processes, (2) their dynamics, (3) the extent to which end-points indicate biological processes, and (4) the costs associated with the assays, which are all addressed by our approach. 48 MEF samples having various combinations of 9 timepoints and 6 UV-C Doses without replication were used
2014-09-01 | E-GEOD-50930 | biostudies-arrayexpress
Project description:An in-vivo experiment with UV-B exposure of the skin of nude, male mice, with and without human-derived p53 variants in their genome to investigate the cellular responses upon UV-induced DNA damage. Essentially, 4 replicate mice were used for each level of UV-exposure. For each mouse a biopsy of the skin was sampled 5-6 times at different recovery time points after UV-pulse exposure, which resulted in paired samples. In total 132 treated and 132 untreated samples were taken from 64 male mice. 264 skin biopsies were taken from 48 mice on 10 timepionts and for 3 different UV-B doses. 3 different genotypes of mice were used, Wild-type (WT; p53+/+), p5372R/72R, and p5372P/72P. Later, it was determined that eight samples came from female mice instead of male mice. Therefore, the eight samples were excluded further analyses (no processed data were generated from these arrays).
2016-03-01 | E-GEOD-63044 | biostudies-arrayexpress
Project description:The goal of this thesis is to study the response of a human keratinocyte cell line (HaCaT cells) after UVB irradiation. In order to develop a system for UV irradiation, we firtstly studied the UV illumination system to find out a stable and reliable condition for UV irradiation experiments. Further, we found out the proper dose of UVB radiation and time points after UVB irradiation by performing MTT assay and trypan blue viability test. According to the results of MTT assay and trypan blue viability test, the cellular activity as well as survival rate of UVB-irradiated cells were in proportion to the radiation doses within a lower UVB dose range. We wanted to find out the possible reasons for this phenomenon by using cDNA microarray. We hope the thesis could be a guide for the following researches, and be useful in the clinical studies about the UV damage. Keywords: dose response and time course Loop-designed microarray experiments were performed in our study. Twenty-one samples are arranges as seven small loops and one large loop, with three and seven microarray slides for each small and large loop, respectively. This set of loop-designed microarray experiment contains one control untreated (non UVB-treated) samples and two UVB-treated samples (one low dose and one high dose UVB-treated) at each time point (total seven time points).
2010-05-16 | E-GEOD-4223 | biostudies-arrayexpress
Project description:Exposure to ultraviolet (UV) irradiation is the major cause of nonmelanoma skin cancer, the most common form of cancer in the United States. UV irradiation has a variety of effects on the skin associated with carcinogenesis, including DNA damage and effects on signal transduction. The alterations in signaling caused by UV regulate inflammation, cell proliferation, and apoptosis. UV also activates the orphan receptor tyrosine kinase and proto-oncogene Erbb2 (HER2/neu). In this study, we demonstrate that the UV-induced activation of Erbb2 regulates the response of the skin to UV. Inhibition or knockdown of Erbb2 before UV irradiation suppressed cell proliferation, cell survival, and inflammation after UV. In addition, Erbb2 was necessary for the UV-induced expression of numerous proinflammatory genes that are regulated by the transcription factors nuclear factor-kappaB and Comp1, including interleukin-1beta, prostaglandin-endoperoxidase synthase 2 (Cyclooxygenase-2), and multiple chemokines. These results reveal the influence of Erbb2 on the UV response and suggest a role for Erbb2 in UV-induced pathologies such as skin cancer. Keywords: time course, ultraviolet irradiation, UV, erbB2, mouse skin The dorsal skin of adult female CD-1 mice was clipped one day before treatment and shaved on the day of treatment. DMSO or 4 mg AG825 dissolved in DMSO was applied topically to the shaved back of the mice 2 h prior to exposure to 10 kJ/m^2 UV or sham irradiation. The UV dose was approximately 30% UVA, 70% UVB and <1% UVC, with a total output of 470 uW/cm^2. Flash frozen skin was removed and total RNA expracted with TRIzol reagent (Invitrogen) and further purified with an RNeasy kit (Qiagen). Amplification, reverse-transcription, biotinylation, and hybridization were all carried out under standard conditions and procedures recommended by the manufacturer.
2006-07-01 | E-GEOD-4066 | biostudies-arrayexpress
Project description:The goal of this thesis is to study the response of a human keratinocyte cell line (HaCaT cells) after UVB irradiation. In order to develop a system for UV irradiation, we firtstly studied the UV illumination system to find out a stable and reliable condition for UV irradiation experiments. Further, we found out the proper dose of UVB radiation and time points after UVB irradiation by performing MTT assay and trypan blue viability test. According to the results of MTT assay and trypan blue viability test, the cellular activity as well as survival rate of UVB-irradiated cells were in proportion to the radiation doses within a lower UVB dose range. We wanted to find out the possible reasons for this phenomenon by using cDNA microarray. We hope the thesis could be a guide for the following researches, and be useful in the clinical studies about the UV damage. Keywords: dose response and time course
2008-11-18 | GSE4223 | GEO
Project description:In molecular biology, the design of mechanistic experiments has to be optimized by considering statistical and biological principles. In contrast to statistical principles, biological principles of experimental design are not universally formulated. In an attempt to pinpoint generally acceptable rules, we investigated the importance of determining the optimal ranges of scale of i.e. dose and time in gene expression experiments. We propose a protocol for executing small scale, genome wide, range finding studies, covering a wide range of the potentially relevant part of the design space to find the optimal ranges of experimentation. This protocol is executed and a proof-of-concept is presented, where this approach is tested for both an in-vitro and an in-vivo study that aim to unravel DNA repair mechanisms provoked after UV radiation. We identified four challenges of range finding studies in omics experimentation; (1) the modularity of biological processes, (2) their dynamics, (3) the extent to which end-points indicate biological processes, and (4) the costs associated with the assays, which are all addressed by our approach.
2014-09-01 | GSE50930 | GEO