Study of UVB responses of SV40 transformed human lung fibroblast: Control vs. UVB irradiated
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: ChengWei Chang
PROVIDER: E-GEOD-41319 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Use DNA microarray technology to discover transciprtional insights of HaCaT for continuous exposure to ELF-EMF We used a loop design in this study (details in the 'loop_design.tiff' supplementary file), cDNA microarray experiment consisted of ten RNA samples, including ELF-EMF exposed, UVB irradiated (positive control), and sham exposed samples.
2014-03-29 | E-GEOD-45631 | 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:Abstract Background: Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair has been described to quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. This repair mechanism has been well characterized in the past using individual target genes. However, the precise mechanism by which RNA polymerase II (Pol II) transcription is affected following UV irradiation during the repair processes genome-wide is not well understood. Results: We investigated the effect of a non-lethal dose of UVB on global DNA-bound Pol II distribution in human cells. We find that about 90% of the promoters of expressed genes show reduced Pol II occupancy 2-4 hours following UVB irradiation, and that the presence of Pol II is restored to “normal”, or higher, levels 5-6 hours after irradiation. We also identified a smaller set of genes, where the presence of Pol II at the promoter regions does not decrease after UVB irradiation, but often increases throughout the entire transcription units. Interestingly, at promoters, where Pol II promoter clearance occurs, TFIIH but not TBP follows the behavior of Pol II suggesting that at these genes TFIIH may be sequestered for DNA repair upon UVB treatment. Conclusions: Thus, our study reveals a global negative regulatory mechanism that targets Pol II transcription initiation on the large majority of transcribed genes following sublethal UVB irradiation, and a small subset of genes (including regulators of repair, cell growth and survival), where Pol II escapes this negative regulation. Following genome-wide RNA Polymerase II redistribution over time upon UVB irradiation
2014-07-25 | E-GEOD-52789 | biostudies-arrayexpress
Project description:The â??small perturbationâ?? approach is critical in studying the â??steady stateâ?? of a biological system. In our experiments, small perturbations were generated by applying a series of repeating intermittent small doses of ultraviolet radiation to a human keratinocyte cell line, HaCaT. The biological response was assessed by monitoring the gene expression profiles using a high reliability and high resolution cDNA microarray system. Following intermittent 10 J/m2 UVB small perturbations, two opposite classes of genes, down-regulated and up-regulated, exhibited an immediate response followed by relaxation between each small perturbation, but were prolonged down- or up-regulated without relaxation while larger doses (233 or 582.5 J/m2) of UVB were applied. A repeated cycle pattern of gene expression following small perturbations is an indication of the existence of steady states. This cycle pattern is suppressed when large perturbations are applied. We believe that this is a universal phenomenon. In our experiments, the functions of up-regulated genes were mainly associated with anti-proliferation, anti-mitogenesis, and apoptosis. On the other hand, down-regulated genes were mainly related to proliferation, mitogenesis, and anti-apoptosis. In conclusion, this study experimentally proves the concept of steady state at the transcription level and demonstrates the feasibility of using small perturbation approaches for investigating steady states. This study could also set a foundation of computational systems biology, which has implicitly used the concept of steady state. Keywords: time course Three UVB exposures are indicated by UV at time points of 0, 8 and 16 hours. T1, T2, T3, T4, T5, and T6 denote the sampling time points. T1, T3 and T5 are allocated 30 minutes after the corresponding UVB irradiation. T2, T4 and T6 are allocated 8 hours after each UVB irradiation. At each sampling time point, two samples (control and UV-irradiated) are collected. See supplementary file Loop_design.pdf for further explanation.
2010-06-24 | E-GEOD-7060 | biostudies-arrayexpress
Project description:Variance in microarray studies has been widely discussed as a critical topic of the identification of differentially expressed gene; however, few studies have addressed the influence of estimating variance. To break intra- and inter-individual variance in clinical studies down to three levels: technical, anatomic, and individual, we designed experiments and algorithms to investigate three forms of variances. As a case study, a group of “inter-individual variable genes” were identified to exemplify the influence of underestimated variance on the statistical and biological aspects in identification of differentially expressed genes. Our results showed that inadequate estimation of variance inevitably led to the inclusion of non-statistically significant genes into those listed as significant, thereby interfering with the correct prediction of biological functions. Applying a higher cutoff value of fold changes in the selection of significant genes reduce/eliminate the effects of underestimated variance. Our data demonstrates that an appropriate evaluation of variance is critical in selecting significant genes of differential expression. If the estimation of precise variance has not been adequately considered in the experimental design, using a higher fold change criteria is one possible solution to overcome the difficulties associated with the identification of significant genes, but it paid by losing the number of selected genes. A total of 11 normal placenta tissues obtained from 9 healthy individuals with term pregnancies, whom underwent cesarean section without labor pain. The first sample group (G1) was composed of samples 1 to 9 of nine individuals. The second sample group (G2) contained 8-1, 8-2 and 8-3, which were three different placental tissues taken from the same individual. The third sample group (G3) consisted of two technical replicates, 8-3_1 and 8-3_2, using the identical RNA pool. Sample 8-3 is estimated by sample 8-3_1 and 8-3_2. Sample 8 is estimated by sample 8-1, 8-2 and 8-3.
2011-03-02 | E-GEOD-27646 | biostudies-arrayexpress
Project description:Renin-angiotensin system regulates cell proliferation, differentiation, apoptosis and tissue remodeling in skin. Previouly, we reported that angiotensin-converting enzyme (ACE) expression and angiotensin II level were enhanced by repeated UVB-irradiation of hairless mice skin, and ACE inhibitor enalapril maleate accelerated recovery of UVB-induced wrinkle. In present study, we analyzed gene expression with DNA microarray and protein distribution with immunofluorecence method to clarify the process of wrinkle repairing with enalapril maleate in UVB-irradiated hairless mouse. In microarray analysis, we detected up-regulation of various extracullular matrix (ECM) genes and ECM related genes. In immunofluorescence, we confirm that type 1 collagen, fibrillin1, elastin, and dystroglycan 1 were decreased by repeated UVB-irradiation and the distribution of these components were improved by enalapril maleate treatment. In addition, ADAMTS2 and MMP-14, these were perticipate in ECM structure formation and degradation, were increased in enalapril maleate-treated mouse skin. While the functions of these molecules in skin is not clear yet, it is suggested that these molecules participate in improvement of wrinkles induced by UVB-irradiation. Male hairless mice of the SKH-1 strain were purchased from Charles River Laboratories Japan, Inc. (Tokyo, Japan). These animals were approximately 6 weeks old at the start of the experiment. They were fed a commercial diet (CRF-1, Oriental Yeast Co., Ltd, Tokyo, Japan) ad libitum and allowed free access to water. The dorsal region of the mouse was repeatedly irradiated with UVB for 10 weeks. Enalapril maleate treatment was started at 1 week after 10-week irradiation. One hundred microliters of 1% w/v enalapril maleate dissolved in 30 vol % ethanol solution or 30 vol % ethanol (control) was applied 5 times a week for 2 consecutive weeks to the whole dorsal skin of each of the mice. All experimental procedures using mice were approved by the Animal Experiment Committee of Tokyo University of Agriculture and Technology (approval number 24-82). The dosal region of the mouse was repeatedly irradiated with UVB for 10 weeks. Enalapril maleate treatment was started at 1 week after 10-week irradiation. One hundred microliters of 1% w/v enalapril maleate dissolved in 30 vol % ethanol solution or 30 vol % ethanol (control) was applied 5 times a week for 2 or 6 consecutive weeks to the whole dorsal skin of each of the mice. Each of the experimental groups comprised 6 mice. After 2- or 6-week drug treatment, skin samples were collected for microarray analysis.
2015-09-24 | E-GEOD-61708 | biostudies-arrayexpress
Project description:xpc-1 mutant animals were treated with 60mJ/cm2 UVB irradiation or mock treated to derive gene expression response to UVB induced DNA damage
2013-08-27 | E-MTAB-1689 | biostudies-arrayexpress
Project description:To address CPD-dependent UVB activities, a model system was established in which transfection of keratinocytes with pseudouridine-modified mRNA (M-NM-(-mRNA) encoding CPD-photolyase resulted in 90% reduction of CPDs within 6 and 24 hours after UVB exposure. Microarray analysis of this model system demonstrated that more than 50 % of the gene expression altered by UVB were changed in a CPD-dependent manner. The expression of most of the CPD-dependent genes was changed at 6 h after UVB as compared to 24 h likely due to the higher CPD levels. Nine genes (ATF3, CCNE1, CDKN2B, EGR1, ID2, PTGS2, RUNX1, SNAI1, SNAI2) regulated by CPDs were selected for further investigation (qPCR, Western blot) based on the microarray data. Gene expression modulated by UVB irradiation in HaCaT keratinocytes was measured at 6 and 24 hours after the exposure to dose of 20 mJ/cm2 UVB. Three independent experiments were performed at each time (6 or 24 hours) using different passages for each experiment.
2015-01-16 | E-GEOD-65034 | biostudies-arrayexpress
Project description:Betaine (trimethylglycine) is a non-toxic, highly water-soluble organic osmolyte widely used in skin care due to its assumed moisturizing and protective properties, but only few studies have addressed its specific effects in skin. Here, the cellular and molecular targets of betaine were analyzed by genome-wide expression analysis in organotypic cultures of rat epidermal keratinocytes (REK). In this model, we also examined whether betaine modifies the impacts of acute UVB exposure. The expression of several genes relevant to epidermal biology, proliferation/differentiation or malignancy as well as solute transport were verified by independent methods (qRT-PCR, western blotting). The data concerning changes in calcium metabolism after UVB exposure has been published separately (Bart et al., Br. J. Dermatol. 171:376-387, 2014). Organotypic cultures of rat epidermal keratinocytes (REK) were prepared by plating cells on a collagen-coated insert (submerged in medium), lifting the confluent cell layer to the air-liquid interface 3 days after plating. These 3D cultures were divided in four treatment groups with three replicates in each: control, betaine (10 mM), UVB (30 mJ/cm2) and betaine + UVB. Betaine was added to the cultures for 11 days, starting from day 4 until sample collection. UVB exposure was performed 24 h prior to sample collection for 2-week-old 3D cultures with a well-formed epidermal layer. For further details on the experimental set-up and characteristics of the UV source, please refer to Bart et al. (Br. J. Dermatol. 171:376-387, 2014) and Rauhala et al. (J. Biol. Chem. 288:17999-18012, 2013).
2015-10-26 | E-GEOD-63004 | biostudies-arrayexpress
Project description:Analysis of gene expression in mouse lens epithelium with or without UVB-irradiation in mouse eye lens. Results provide insight into a role for the respons to UVB-irradiation in lens epithelial cells.
2019-02-13 | GSE126294 | GEO