Ovarian transcriptional profiles of four mouse strains
Ontology highlight
ABSTRACT: The transcriptional profiles of ovarian tissue from four laboratory mouse-inbred strains were obtained with NIA15K-cDNA microarrays and then correlated with the divergent spontaneous ovarian tumor rates and reproductive parameters reported for each strain. Four test samples and one reference sample - common reference design- dye swap - 5 to 6 replicates per sample - test samples pooled from 4-6 animals , 23 arrays
Project description:Transcriptional profiling of human embryonic kidney 293 cells comparing transfected control pEGFP-C1 (empty vector) with pEGFP (survivin vector). One condition experiment; survivin transfected cell as test sample vs empty vector transfected cell as reference; one dye swap replicate
Project description:Cell competition promotes the elimination of weaker cells from a growing population. Here we investigate how cells of Drosophila wing imaginal discs distinguish “winners” from “losers” during cell competition. Using genomic and functional assays we have identified Maxwell`s Demon (Mwd), a cell membrane protein conserved in multicellular animals. Our results suggest that the membrane protein Mwd is a dedicated component of the cell competition response that is required and sufficient to label cells as “winners” or “losers”. In Drosophila, the mwd locus produces three isoforms, mwdubi, mwdLose-A and mwdLose-B. Basal levels of mwdubi are constantly produced. During competition the mwdLose isoforms are upregulated in prospective loser cells. Cell-cell comparison of relative mwdLose and mwdubi levels ultimately determine which cell undergoes apoptosis. This “extracellular code” may constitute an ancient mechanism to terminate competitive conflicts among cells. Two samples have been analysed: tub>dmyc>Gal4 transgene cells (competitor) and tub>cd2>Gal4 control cells (non competitor) at different time points (0, 12, 24 and 48 hours). Each experiment was replicated 6 times, three of them by dye swap.
Project description:Transcriptional profile of esx-3 conditional mutant strain (TB79) vs its parental strain (TB38) grown in 7H9 in presence of 100ng/ml Atc for 48h One experimental condition. 2 independent biological replicates. One replicate per array.
Project description:to see if CCPRCC has a distinct miRNA profile from CCRCC and PRCC miRNA v.2.0 chips on two portions of five CCPRCC cases (total 10 samples), three portions of two CCRCC cases and a further three CCRCC cases (total 9 samples), and five type I PRCC samples; a total of 24 samples
Project description:An ovarian cancer cell line study to identify possible trends between chromosomal aberrations depicted from CGH microarray profiling with expression profiling. CGH microarray profiles of a panel of ovarian cancer cell lines will be analysed and 10 cell lines with chromosomal aberrations of recurrent regions (with the strongest trend) will be taken forward for further expression array analysis to identify candidate genes. CGH microarray analyses will restrict the regions of aberrations with high resolution and accurracy, combined with expression array analysis to pinpoint candidate genes that will relate to the amplified and deleted regions. Identified candidates will allow the better understanding of mechanisms and specific pathways involved in ovarian cancer development. A collection of 31 cell lines in the laboratory will be used. CGH microarray profile analyses will be carried for all, a selection process will be used to separate the groups such as the subtypes of the cell line. An analysis program will be used to depict recurrent regions and 10 cell lines will be taken forward for further expression array analysis to identify candidate genes.
Project description:Anaylsis differentially expressed genes of mouse peri-implanted uteri comparing pre-implantation uteri (Day2, Day3 and Day4) with post-implantation uteri (Day6, Day7 and Day8) by microassay. This study has built a meaningful basis for future investigation in elucidating the molecular nature of maternal-fetal interactions during pregnancy establishment and maintenance. Pre-implantation uteri VS. Post-implantation uteri. Three biological replicates of each experiments: pre-implantation uteri (Day2, Day3 and Day4): 234, 234①, 234②; 3 mixture of post-implantation uteri (Day6, Day7 and Day8): 678, 678①, 678②. Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each sample.
Project description:The physiological basis of the hypothesis that temperature is the primary governing factor of bacterial cell inactivation under otherwise non-growth permissive conditions was investigated. Application of simultaneous low pH (pH 3.5) and low water activity (aw = 0.9; 2.5 M NaCl) conditions, applied to L. monocytogenes strains Scott A and FW03/0035, and increasing incubation temperature from 25°C up to 45°C resulted in increased permeability to ethidium homodimer-1 and corresponded to accelerated declines in esterase activity and ATP basal levels but did not result in autolysis. Triphasic survival curves were readily observable when sufficiently large cell populations were inactivated at 25°C and 35°C; indicative of a mixture of sensitive and resistant sub-populations. Enrichment-based recovery experiments however indicate that the stress conditions eventually lead to complete loss of reproductive capacity, potentially corresponding to an irreversible collapse of pH homeostasis. Transcriptomic analyses were used to further obtain insights into the physiology of the inactivation process occurring at 25°C. RT-PCR, rifampin-enforced decay and microarray experiments revealed transcripts of tufA and other genes become substantially more stable during inactivation during exposure to combined low pH/aw and during non-growth permissive temperature exposure. Gene transcripts were delineated through K-means clustering that appear to be important for initial survival of combined low pH/aw and include an overrepresentation of SigB-activated genes, the response of which fades with increasing time of inactivation exposure. The microarray component of the experiments had the aim of determining: i) Gene expression responses of L. monocytogenes strain Scott A when exposed to a non-growth permissive environment consisting of a broth system acting as a food simulated environment adjusted to low pH (pH 3.5) and low water activity (2.5 M NaCl). ii) To examine the trend in gene expression over time under inactivating (killing) conditions by applying gene set (functional and regulatory) expression trend analysis and K-means cluster analysis. iii) To correlate this data to other physiological and mRNA quantification (real-time-PCR) data. Experimental design: Two biologically replicated control cultures (each with two technical replicate sper chip) were labelled with Cy3 for each treatment sample for a total of 4 pairs of biological replicates. The treatments consisted of treated (inactivated in brain-heart infusion broth at pH 3.5 and water activity 0.9) L. monocytogenes cells with two biological replicates (each with two technical replicates per chip) labelled with Cy5. The time course (incubation time under inactivating conditions) of treatments was âinitialâ (20 minutes), 24 h, 48 h, and 72 h.
Project description:The relevance of immune-endocrine interactions to the regulation of ovarian function in teleosts is virtually unexplored. As part of the innate immune response during infection, a number of cytokines such as tumor necrosis factor α (TNFα) and other immune factors, are produced and act on the reproductive system. However, TNFα is also an important physiological player in the ovulatory process in mammals. In the present study, we have examined for the first time the effects of TNFα in vitro in preovulatory ovarian follicles of a teleost fish, the brown trout (Salmo trutta). In control and recombinant trout TNFα (rtTNFα)-treated granulosa cells, we examined the percentage of apoptosis by flow cytometry analysis and cell viability by propidium iodide (PI) staining. Furthermore, we determined the in vitro effects of rtTNFα on follicle contraction and testosterone production in preovulatory trout ovarian follicles. In addition, we analyzed the gene expression profiles of control and rtTNFα-treated ovarian tissue by microarray and real-time PCR (qPCR) analyses.Treatment with rtTNFα induces ovarian cell apoptosis, decreases granulosa cell viability and stimulates the expression of genes known to be involved in the normal ovulatory process in trout. In addition, rtTNFα causes a significant increase in follicle contraction and testosterone production. Also, using a salmonid-specific microarray platform (SFA2.0 immunochip) we observed that rtTNFα induces the expression of genes known to be involved in inflammation, proteolysis and tissue remodeling. In view of these results, we propose that TNFα could have an important role in the biomechanics of follicle weakening, ovarian rupture and oocyte expulsion during ovulation in trout, primarily through its stimulation of follicular cell apoptosis and the expression of genes involved in follicle wall proteolysis and contraction. Reproductively mature female brown trout (Salmo trutta) from a cultured stock at the Piscifactoria de Bagà (Generalitat de Catalunya, Bagà , Spain) were kept under natural conditions of temperature and photoperiod. Fish at the preovulatory stage (according to the position of the germinal vesicle (GV) in oocytes that were cleared using a solution previously described), were anesthesized in 3-aminobenzoic acid ethyl ester (0.1 g/l; Sigma, Alcobendas, Spain) dissolved in fresh water, and the fish were sacrificed by concussion prior to the collection of the ovaries. The dissected ovaries were immediately used for the various in vitro assays. After dissection, brown trout preovulatory ovaries were placed in Hank´s balanced salt solution (HBSS) and individual ovarian follicles were manually separated with forceps from each ovary on ice, as previously described. To collect ovarian tissue for RNA extraction, preovulatory follicles from each of a total of three females were incubated (400 follicles/50 ml) in HBSS-BSA in the absence or presence of rtTNFα (100 ng/ ml, dissolved directly in HBSS-BSA), at 15ºC for 24 h with gentle shaking (100 rpm). At the end of the incubation follicles (previously de-yolked by gentle pressure) were removed, flash frozen in liquid nitrogen and stored at -80ºC until assayed.
Project description:microRNA profiling of mouse testis comparing treatment with doxorubicin to vehicle only control (published in Toxicology Research, DOI: 10.1039/C6TX00078A) Two-condition experiment, doxorubicin vs control at 3 time points (1wk, 4wk and 7 wk following treatment). Biological replicates: 12 control, 12 doxorubicin (implementing a dye swap design of n=6 forward and n=6 reverse). One replicate per dual colour array (total of 36 arrays).
Project description:Transcriptional profiles from Acidithiobacillus ferrooxidans type strain ATCC23270 grown in the presence of iron or elemental sulfur as energy source until mid logarithmic phase were compared. Cells were harvested after 48 hs of growth in 9K-FeII pH 1.6 and after 120 hs of growth in 9K-S0 pH 3.5. Pellets were washed to remove precipitates, frozen and stored at -80C until RNA extraction.<br><br>In toto 8 different hybridizations were performed using 4 independent biological samples of A. ferrooxidans (with dye-swap), 4 arrays of array design FCV-CNRS AFE Oligoarray v.1 and 4 arrays of array design FCV-CNRS AFE Oligoarray v.2. This experimental design produced 8 raw data files and 1 transformed and/or normalized data file.