Project description:Raw RNAseq data from ferns sampled in Singapore. Organ specific samples were selected for assembly via denovo assembly for comparative transcriptomics.
Project description:This series of mouse expression database represents samples contributed by researchers at University of Cincinnati and Cincinnati Children's Hospital profiles Keywords: other
Project description:The Rfam database is a RNAcentral consortium member database which holds the collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).
Project description:This series of mouse expression database represents samples contributed by researchers at University of Cincinnati and Cincinnati Children's Hospital profiles
Project description:TK6 cells were exposed to various perturbations and then the transcriptome profiles were collected at 4 hours to assemble a reference database to generate a Genotoxic / Nongenotoxic classifier using the nearest shrunken centroids method.
Project description:A small database of transcription profiles called PgGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PgGenExpress. In conifer trees, dehydrins and late embryogenesis (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs.
Project description:As part of the EcoToxChip project, 49 distinct exposure studies were conducted on three lab model species (Japanese quail, fathead minnow, African clawed frog) and three ecologically relevant species (double crested cormorant, rainbow trout, northern leopard frog), at multiple life stages (embryo, adult), exposed to eight chemicals of environmental concern (ethinyl estradiol-EE2, hexabromocyclododecane-HBCD, lead-Pb, selenomethionine-SeMe, 17β trenbolone-TB, chlorpyrifos-CPF, fluoxetine-FLX, and benzo [a] pyrene-BaP. Whole transcriptome analyses were conducted on these samples resulting in a rich RNA seq dataset covering various species, life stages and chemicals, which is one of the largest purposeful complications of RNA seq data within ecotoxicology. Recently, a unified bioinformatics platform of relevance to ecotoxicology, EcoOmicsAnalyst and ExpressAnalyst, was developed to facilitate RNA Seq analysis of non-model species lacking a reference transcriptome. The platform uses the Seq2Fun algorithm to map RNA-seq reads from eukaryotic species to an ortholog database comprised of protein sequences from >600 eukaryotic species (EcoOmicsDB) with a translated search. The availability of these tools presents a unique opportunity to examine the EcoToxChip RNA Seq dataset for cross species comparisons. This work shows the potential of the EcoOmicsAnalyst and Seq2Fun platform to facilitate fast and simple analysis of RNA Seq datasets from non-model organisms with unannotated genomes and conduct comparative transcriptomic analysis across various species and life stages for cross-species extrapolation.
Project description:Pesticides are widely used to protect growth of crops and prevent the spread of diseases. However, more and more pest insects have developed resistance to chemical pesticides along with the long-term application of the pesticides. It is very important to explore the molecular mechanisms of insecticide resistance not only for reversing the resistance in insects, but also for finding out new function targets of the insecticides. Recently, the next-generation sequence technique has become an effective tool to screen resistance genes and has developed transcriptome profiles of various species. However, a comprehensive database to collect these transcriptome data remains poorly developed. In this study, we constructed a database for insect resistance called IRdb, which contains gene count data from various insect species analyzed by a unified process. In addition to the gene data, IRdb also contains 430 unique resistance proteins (experimentally verified proteins manually extracted from literature). Users can discriminate the resistance proteins by submitting fasta sequence of proteins of interest, which can provide clues to detect resistance proteins. The application of resistance protein part in IRdb indicates the accuracy of prediction of IRdb by extracting CTD features and employing random forest. The database IRdb online web server (http://120.27.24.199:20609/) was provided for users to download the transcriptome and protein data for resistance of insects to insecticides and to predict potential resistance proteins.
Project description:TK6 cells were exposed to various perturbations and then the transcriptome profiles were collected at 4 hours to assemble a reference database to generate a Genotoxic / Nongenotoxic classifier using the nearest shrunken centroids method. TK6 cells were exposed to various perturbations and then the transcriptome profiles were collected at 4 hours to assemble a reference database to generate a Genotoxic / Nongenotoxic classifier using the nearest shrunken centroids method.