Expression data of worms under different caloric restriction mimetic treatments
ABSTRACT: We used microarray analysis to further our understanding of the mode of action of the well know caloric restriction mimetic rapamycin and the compound Allantoin first studied in the context of aging in this study. His work helps build on our understanding of potential caloric restriction mimetics predicted from our bioinformatic aproach of quering the Connectivity Map, a database of drug-induced gene expression profiles, using the transcriptional profile of CR to identify drugs that induce a similar or opposite gene expression profile. Wild type worms of eat-2 mutants (a model of caloric restriction) were treated with the compounds of study with 2% DMSO or DMSO alone to serve as controls. All samples were peformed in triplicate.
Caloric restriction (CR), a reduction in calorie intake without malnutrition, retards aging in several animal models from worms to mammals. Developing CR mimetics, compounds that reproduce the longevity benefits of CR without its side effects, is of widespread interest. Here, we employed the Connectivity Map to identify drugs with overlapping gene expression profiles with CR. Eleven statistically significant compounds were predicted as CR mimetics using this bioinformatics approach. We then test ...[more]
Project description:Triple negative breast cancer (TNBC) is an incurable disease with poor prognosis. At this moment, therapeutic options are limited to chemotherapy and no targeted agent has reached the clinical setting. Bromodomain and extraterminal (BET) inhibitors are a new family of compounds that inhibit bromodomain containing proteins affecting the expression of transcription factors (TFs), therefore modifying the expression of relevant oncogenic genes. We decided to performed gene-set enrichment analyses to get insights into the mechanism of action of these compounds. We treated cells with JQ1 and extracted RNA at 12 and 24 hours.
Project description:The purpose of this study was to chacterise the effect of KDM1A knocking down on genome-wide gene expression in human NSCLC cells in vivo. Affymetrix human transcriptome array 2.0 was used to profile the transcriptome of xenograft tumors derived from PC9 cells stably expressing either ShRNA KDM1A or ShRNA control. These cells were subcutanously injected into the right axillary of the mouse, and allowd to grow for 5 weeks to form xenograft tumors. Although KDM1A is up-regulated in NSCLC, but key genes and pathways regulated by KDM1A was not well-understood in NSCLC. Using this approach, we have shown that KDM1A repressed or activated a distinctive set of pathways and key target genes in vivo. This first comprehesive study of transciptome profile upon KDM1A koncking-down in vivo highlights the distinctive pathways regulated by KDM1A during NSCLC tumorigenesis, and it will help to identify new therapeutic targets for NSCLC treatment. Xenograft tumors derived from two cell lines: PC9 cells stably expressing ShRNA KDM1A or ShRNA control. We extracted total RNA from 3 independent xenograft tumors per cell line.
Project description:Ectopic expression of DNMT3L in Drosophila causes melanotic tumor in the transgenic flies from fifth generation onwards. We used microaarray data analysis to look for the genes and pathways which are affected on ectopic expression of DNMT3L in Drosophila. Drosophila third instar larvae were selected at particular stages of development for RNA extraction and hybridization on Affymetrix microarrays.
Project description:The experiment aims at a characterization of gene expression changes in duodenum during caloric restriction. The C57BL6 mice were restricted their food intake to 75% of their normal daily portion. The food was delivered daily around 4-6pm for 14 days. The mice were housed with free access to water. The control age-matched mice were fed ad libitum. The publication associated with this dataset concerns WT mice only. However, the experiment and microarray data normalization was performed for samples of WT and PPARgVillinCRE mice together. Thus for analysis reproducibility reasons data of all samples is made available.
Project description:Expression of the mirn23a cluster in murine hematopoietic progenitors blocks B cell development. Overexpressed individual cluster members miRs-23a, 24-2, and -27a in 70/3 mouse pre-B cells in order to examine changes in gene expression that would potentially reveal targets of the miRs relevant to hematopoiesis. Two independent 70Z/3 cell lines for each experimental group were generated (MSCV, miR-23a, miR-24-2, and miR-27a). RNA was generated and hybridized on Affymetrix microarrays.
Project description:Transcriptome analysis of early adipogenesis induced by basal adipogenesis medium(AM) and AM+Bex for 2 days in C2C12 cells Global gene expression profiling has shown Bex induced adipogenic genes expression change We analyzed 4 samples from basal adipogenesis medium(AM) and AM+Bex(10uM) treated C2C12 cells using the Affymetrix Mouse Gene 1.0 ST platform. Array data was processed by Affymetrix Expression Console and Transcriptome Analysis Console (TAC) software.
Project description:The molecular mechanisms involved in the coordinate regulation of the metabolic and structural determinants of muscle endurance are still poorly characterized. To help elucidate the role of ERRa in this process, gene expression arrays were employed resulting in the identification of ERRa-dependent genes involved in metabolic processes, oxidative stress response, maintenance of muscle fiber integrity and neovascularization. Gastrocnemius (n=3) isolated from 2-3 month old WT and ERRa-null mice under pre-exercise (sedentary) and post-exercise (2 h following acute exhaustion on a treadmill) were used for gene expression studies using Affymetrix mouse 2.0 gene ST arrays.