Project description:Transcroptomic analysis of the cells grown on pyruvate in the sterilized soil and those grown on pyruvate to mid-exponenyial phase in a liquid medium 4x dual channel slides.
Project description:Transcriptomic analysis of the cells grown on biphenyl in the sterilized soil and those grown on biphenyl to mid-exponential phase in a liquid medium 4x dual channel slides.
Project description:Transcriptomic analysis of the cells grown on biphenyl on a filter placed on a minimal agar medium and those grown on biphenyl to mid-exponential phase in a liquid medium 3x dual channel slides.
Project description:Here we report the first transcriptomic analysis of a Gram-positive bacterium to desiccation. Filtered RHA1 cells incubated at either low relative humidity (20%), as an air drying treatment, or high relative humidity (100%), as a control, were transcriptionally profiled over a comprehensive time series. Keywords: stress response time course Three biological replicates from both the desiccation and control experiments were analyzed using two-colour microarrays. Over a time series for each experiment, Cy-labelled cDNA from treated and time-zero cells were hybridized, with a dye swap for one of the replicates.
Project description:In Drosophila, X chromosome dosage compensation requires the male-specific lethal (MSL) complex, which associates with actively transcribed genes on the single male X chromosome to upregulate transcription approximately 2-fold. We found that on the male X chromosome, or when MSL complex is ectopically localized to an autosome, histone H3K36 trimethylation (H3K36me3) is a strong predictor of MSL binding. We isolated mutants lacking Set2, the H3K36me3 methyltransferase, and found that Set2 is an essential gene in both sexes of Drosophila. In set2 mutant males, MSL complex maintains X specificity but exhibits reduced binding to target genes. Furthermore, recombinant MSL3 protein preferentially binds nucleosomes marked by H3K36me3 in vitro. Our results support a model in which MSL complex uses high-affinity sites to initially recognize the X chromosome and then associates with many of its targets through sequence-independent features of transcribed genes. Keywords: ChIP-chip ChIP-chip experiments were performed on custom Nimblegen arrays (GPL5636). Each array contained 388,000 oligonucleotide probes covering all of the X and the 2L chromosomes, with a 100 bp resolution (50mer probes with 50 bp gaps). The design was based on FlyBase 3.2. For the superspreading experiments, an additional array was used that contains the entire X chromosome and 3R (GPL5660). MSL complex binding sites on both arrays are the same and signal on the 3R chromosome was at background level.
Project description:Time is often not characterized as a variable in ecotoxicogenomic studies. In this study, the temporal kinetics in gene expression were determined during exposure to crude oil and a subsequent recovery period. Juvenile rainbow trout, Oncorhynchus mykiss, were exposed for 96 hours to the water accomodated fractions of 0.4, 2 or 10 mg l-1 crude oil loadings. Following 96 h of exposure, fish were transferred to recovery tanks for 96 h. Gill and liver samples were collected after 24 and 96 h of exposure, and after 96 h of recovery for RNA extraction and microarray analysis. Fluorescently labeled cDNA was hybridized against matched controls, using salmonid cDNA arrays. Each exposure scenario generated unique patterns of altered gene expression. More genes responded to crude oil in the gill than in liver. In the gill, 1137 genes had altered expression at 24 hours, 2003 genes had altered expression levels at 96 h of exposure, yet by 96 h of recovery, no genes were significant ly altered in expression. The Gene Ontology terms associated with gill-responsive genes implicated membrane narcosis, a toxic mechanism for crude oil. By contrast, in the liver at 10 mg l-1, only five genes were changed at 24 h, yet 192 genes had altered expression after 96 h recovery. At 2 mg l-1 in the liver, many genes had altered regulation at all three timepoints. The 0.4 mg l-1 loading also showed 289 genes upregulated at 24 h after exposure. The Gene Ontology terms associated with altered expression in the liver suggested that the processes of protein synthesis, xenobiotic metabolism, and oxidoreductase activity were altered. The concentration-responsive expression profile of cytochrome P450 1A, a biomarker for oil exposure, did not predict the majority of gene expression profiles in any tissue or dose, since direct relationships with dose were not observed for most genes. While the genes and their associated functions agree with known modes of toxic action for crude oil, the gene lists obtained do not agree with our previously published work, presumably due to array analysis procedures. These results demonstrate that changes in gene expression with time and dose should be characterized in controlled laboratory settings before responses from field collected organisms are interpreted, and that processes for analyzing microarray data need to be developed such that standardized gene lists are developed, or that analysis is gene list independent before arrays are as a monitoring tool. Two channel experiment; Control versus exposed (samples were time matched). 3 biological replicates, two technical replicates for both exposed and control fish. Exposed and cotrol samples were paired so that fish had been sacrificed at the same time, but otherwise, samples were paired at random. One replicate per array