Project description:Next Generation Sequencing in cancer: a feasibility study in France to assess sample circuit and to perform analyzes within a limited time.
| 2274538 | ecrin-mdr-crc
Project description:Lactobacillus isolated from commercial probiotics
Project description:FastQ files from 16S sequencing of fecal samples from pancreatic cancer xenografted mice not treated (CTRL) and treated with chemotherapy (GEM+nab-PTX), probiotics (PRO) and chemotherapy + probiotics (GEM+nab-PTX+PRO)
Project description:The objective of this study is to optimize the search by next-generation sequencing (NGS) mutations in the KRAS, BRAF and NRAS on circulating tumor DNA and compare the genetic profiles obtained with those from tumors embedded in paraffin
Project description:IPNV is a viral pathogen causing losses in commercial aquaculture of Atlantic salmon. This study was performed to examine transcriptomic responses to IPNV and to compare them with changes caused with other viruses.
Project description:Next Generation Sequencing (NGS) was performed by commercial agreement with Beijing Genomics Institute (BGI). We have evaluated the miRNA profiles of mouse testis during the spermatogenic progression after ex vivo culture. We have observed that as long as spermatogenesis progress, miRNA expression decreases. However, we have identified some miRNAs that did not follow this expression profile, like miR-34c-5p and miR-449a-5p, with a higher expression in samples where the spermatogenic process was more advanced, which suggest important roles at the last stages of spermatogenesis.
Project description:We have adapted a commercial assay that employs mRNA quantification based on the frequency of PCR amplicons determined by next-generation to a high-throughput semi-conductor sequencing platform (Ion-Torrent Proton). We show parallel amplification of pathway derived transcript sets/genes in 12 reference RNA samples followed by sequence-based quantification covering a dynamic range of five orders of magnitude with low technical variation.
Project description:Domestication of finfishes is a key element toward sustainable expansion of aquaculture sector. However, huge gap in knowledge on the mechanisms of adaptability of fish to the culture environment, being the first step toward successful domestication, exists. This affects the overall production capacity which is hindered, among others, by lowered reproductive capacity of domesticated stocks, including pikeperch – a highly valued commercial freshwater fish species. Transcriptomic profiling of embryos was found to be useful tool significantly contributing into understanding domestication process in aquaculture. Up to now there is no data on transcriptomic profiling of unfertilized eggs in any fish species as well as on pikeperch, in general. Using next generation sequencing the first complex transcriptome of pikeperch have been obtained (with 40,246 unique protein-coding genes). Next, specifically designed, pikeperch-specific microarrays (Agilent technologies) were developed (with 35,343 unique probes) and transcriptomic profiling of eggs coming from wild and domesticated populations (all characterized by high quality) was performed. From among 17,543 genes found to be expressed in eggs of pikeperch 710 were found to be differentially expressed. Functional, enrichment analysis revealed that the most enriched processes represented by the set of genes identified were developmental process, regulation of phosphorylation and nervous system development. The results of the present study provides a new insight into the processes being directly involved in the successful domestication of finfishes. It can be suggested that all the identified processes were pre-determined by the maternally derived set of genes contained already in the unfertilized eggs, what has never been reported to date. In addition to that, it has been shown for the first time that among the most important processes being affected by the domestication the post translation modifications of proteins along with development of the nervous system were identified. This allows to suggest that fish behavior should be considered as a very important trait for selection for aquaculture purposes in pikeperch.
Project description:Due to the increase in stocking density, eutrophication of water quality, and high-temperature conditions aggravate the possibility of hypoxia, and inevitably lead to hypoxic stress, affecting the development of its aquaculture industry. We simulated severe hypoxia stress conditions and constructed two different hypoxia tolerance groups. We used next-generation sequencing to analyze the mRNA expression profiles of the brain and liver under hypoxia to clarify the main pathways and metabolic pathways involved in hypoxia, to systematically reveal the reasons for the differences in hypoxia tolerance among different groups.
2021-12-31 | GSE163685 | GEO
Project description:Roseobacter probiotics support a balanced aquaculture microbiome
