Project description:Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we present ABI's OpenArray and qPCR systems. TCDD-sensitive (Long-Evans) and TCDD-resistant (Han/Wistar) rats were used in both time-course and dose response studies to asses the transcriptomic response to TCDD-insult. The time-course experiment saw animals recieve a single dose of 100ug/kg TCDD or corn oil vehicle followed by euthanasia and tissue collection at various time-points. Animals in the dose-response experiment recieved a single dose of TCDD at varying concentrations or corn oil vehicle, followed by euthanasia and tissue collection 19 hours post-treatment. Each treatment group contained 4-5 biologicial replicates.

2012-10-18 | E-GEOD-41388 | biostudies-arrayexpress

Transcriptomic responses to iron bioavailability from virus-mediated lysates in marine prokaryotes

Project description:Previous studies have demonstrated that the iron content in marine heterotrophic bacteria is comparatively higher than that of phytoplankton. Therefore, they have been indicated to play a major role in the biogeochemical cycling of iron. In this study, we aimed to investigate the potential of viral lysis as a source of iron for marine heterotrophic bacteria. Viral lysates were derived from the marine heterotrophic bacterium, Vibrio natriegens PWH3a (A.K.A Vibrio alginolyticus). The bioavailability of Fe in the lysates was determined using a model heterotrophic bacterium, namely, Dokdonia sp. strain Dokd-P16, isolated from Fe-limited waters along Line P transect in the Northeastern Pacific Ocean. The bacteria were grown under Fe-deplete or Fe-replete conditions before being exposed to the viral lysate. Differential gene expression following exposure to the viral lysate was analyzed via RNA sequencing to identify differentially expressed genes under iron-replete and iron-deplete conditions. This study would provide novel insights into the role of viral lysis in heterotrophic bacteria in supplying bioavailable iron to other marine microorganisms under iron-limiting and non-limiting conditions. First, the marine heterotrophic bacterium genome, Dokdonia sp. strain Dokd-P16, was sequenced to provide a genomic context for the expression studies. Subsequently, the relative gene expression in Dokdonia sp. strain Dokd-P16 grown under Fe limiting and non-limiting conditions were analyzed. This transcriptomic approach would be utilized to elucidate genes regulated by Fe availability in Dokdonia sp. strain Dokd-P16, which indicate its Fe-related response viral lysate exposure. Taken together, in this study, the transcriptomic responses of Fe-limited and non-limited marine heterotrophic bacteria were analyzed, which provided novel insights into the biological availability of Fe from the viral lysates.

2021-11-01 | GSE166618 | GEO

Rubrobacter radiotolerans DSM 5868

Project description:High radiation-resistant, pink-pigmented, thermophilic bacteria

| PRJNA37865 | ENA

NanoString analysis of a rat liver mRNA panel following TCDD treatment

Project description:Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we fill that gap by comparing two key medium-throughput platforms M-bM-^@M-^S NanoStringM-bM-^@M-^Ys nCounter Analysis System and ABIM-bM-^@M-^Ys OpenArray System M-bM-^@M-^S to gold-standard quantitative real-time RT-PCR. TCDD-sensitive (Long-Evans) and TCDD-resistant (Han/Wistar) rats were used in both time-course and dose response studies to asses the transcriptomic response to TCDD-insult. The time-course experiment saw animals recieve a single dose of 100ug/kg TCDD or corn oil vehicle followed by euthanasia and tissue collection at various time-points. Animals in the dose-response experiment recieved a single dose of TCDD at varying concentrations or corn oil vehicle, followed by euthanasia and tissue collection 19 hours post-treatment. Each treatment group contained 4-5 biologicial replicates.

2013-12-31 | E-GEOD-43251 | biostudies-arrayexpress

Proteomics characterization of the non-model microorganism: Nannochloropsis gaditana.

Project description:Nannochloropsis gaditana is a microalgae of the phylum eustigmatophyceae that has been reported from fresh and brackish waters. This species has been widely cultured, mainly directed to biofuel production, due to its capacity to produce and accumulates high amounts of lipids under different culturing conditions. Furthermore, nowadays N. gaditana is being used as fish and mollusc food in aquaculture facilities. Besides, microalgae are recognized protein producers, thus, are posited as an alternative protein source that could be very valuable in areas such as agri-food or biomedicine. In this sense, seas and oceans had showed their great potential for innovation, being the main focus of the initiative Blue Growth from EU. Thereby, marine biotechnology will provide of new pharmaceuticals or industrial products from marine biomass. In order to study the whole proteome of Nannochloropsis gaditana, a proteomic approach was initiated using fresh and atomized microalgae samples, as the main commercial forms. Around 7500 peptides were detected, getting 1950 protein identification hits. Qualitative and quantitative differences were analysed. The identified proteins were categorized according to gene ontology classification. In this study, it has been developed and described the first proteomic analysis of the microalgae Nannochloropsis gaditana, containing an important number of identified proteins that may have a relevant role in different agri-food and biomedical processes.

2018-11-07 | PXD008499 | Pride