Project description:Transcriptome analyses of 24-hour zebrafish embryos from the Tuebingen line were performed using the Affymetrix GeneChip Zebrafish Genome Array (GeneChip 430)
Project description:Strain-specific CNV in zebrafish as determined by competitevly hybridizeing AB, Tuebingen, or WIK individuals exposed to PCB-126, vehicle control, or naïve versus pooled Casper strain
Project description:Strains of commonly used wildtype zebrafish (Danio rerio) have both shared and unique genomic features such as SNPs and copy number variants. Unfortunately, exact lab strains are often unreported in the literature and the replication of studies in zebrafish may be negatively impacted by this fact. These data were collected to assess hepatic mRNA expression patterns between three common zebrafish strains (AB, Tuebingen, and WIK) to establish baseline differences across strains and between sexes.Baseline mRNA expression was analyzed in six individuals pers strain (three males and three females) using Agilent 4x44K gene expression microarrays . These data highlight the complexity of variation that exists within zebrafish and underscore the value of this model system as a valid representation of normal variation present in other species, including humans.
Project description:Common strains of wildtype zebrafish (Danio rerio) have unique genomic features including SNPs and CNV, but strain information often goes unreported in the literature. As a result, the confounding effects of interstrain variation makes repetition of studies in zebrafish challenging. Here we analyze hepatic mRNA expression patterns between three common zebrafish strains (AB, Tuebingen (TU), and WIK) using Agilent 4 × 44 K gene expression microarrays to establish baseline mRNA expression across strains and between sexes. We observed wide variation in sex-specific gene expression within AB and WIK strains (141 genes in AB and 67 genes in WIK), but no significant variation between sexes within TU. After partitioning the dataset into male and female subsets, we detected 421 unique mRNA transcripts with statistically significant differential expression; 269 mRNA transcripts varied between males, 212 mRNA transcripts varied between females, and 59 mRNA transcripts varied across the three strains, regardless of sex. It is not surprising that mRNA expression profiles differ between sexes and strains, but it is imperative to characterize the differences. These results highlight the complexity of variation within zebrafish and underscore the value of this model system as a valid representation of normal variation present in other species, including humans.
Project description:Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information. We further analyzed zebrafish CNVs using pooled samples of 10 zebrafish each from three laboratory strains (AB, Tubingen, and WIK) to identify strain specific CNVs between groups.
Project description:The yeast Saccharomyces cerevisiae is a powerful model system that is often used to expand our understanding of cellular processes and biological functions. Although many genetically well-characterized laboratory strains of S. cerevisiae are available, they may have different genetic backgrounds which can confound data interpretation. Here, we profile and compare the proteomes of two common laboratory yeast background strains, W303 and BY4742, in both exponential and stationary growth phases using isobaric tag-based mass spectrometry. We quantified over 4,400 proteins, hundreds of which showed differences in abundance between strains and/or growth phases. Moreover, we used proteome-wide abundance to profile the mating type of the strains used in the experiment, the auxotrophic markers and associated metabolic pathways, as well as to investigate differences in particular classes of proteins, such as the pleiotropic drug resistance (PDR) proteins. This study is a valuable resource that offers insight into mechanistic differences between two common yeast background strains and can be used as a guide to select a background that is best suited for addressing a particular biological question.
Project description:Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information. We further analyzed zebrafish CNVs using pooled samples of 10 zebrafish each from three laboratory strains (AB, Tubingen, and WIK) to identify strain specific CNVs between groups. 10 zebrafish from 3 laboratory strains were pooled and run against the other pooled samples resulting in three array combinations.
Project description:The environmental stresses and inhibitors encounted by Saccharomyces cerevisiae strains are main limiting factors in bioethanol fermentation. Investigation of the molecular mechanisms underlying the stresses-related phenotypes diversities within and between S. cerevisiae populations could guide the construction of yeast strains with improved stresses tolerance and fermentation performances. Here, we explored the genetic characteristics of the bioethanol S. cerevisiae strains, and elucidated the genetic variations correlated with its advantaged traits (higher ethanol yield under sever conditions and better tolerance to multiple stresses compared to an S288c derived laboratory strain BYZ1). Firstly, pulse-field gel electrophoresis combined with array-comparative genomic hybridization was used to compare the genome structure of industrial strains and the laboratory strain BYZ1.
