Project description:We used single-cell sequencing data and imaging to investigate Eukaryotic plankton from environmental marine samples collected from Coogee, NSW, Australia.
2024-08-18 | GSE274796 | GEO
Project description:Diazotrophs in the Southern California Current System
Project description:The present study performed the proteomic and biological activities of Peruvian Crotalus durissus, an endangered species reported to cause neuro and myotoxic symptoms. Due to the severity of its envenomation and to its geographical location, Peruvian Crotalus durissus is considered of public health importance in Peru. Snakebite treatment depends on rapid administration of appropriate antivenom. In this sense, the recognition of Peruvian Crotalus durissus venom (PCdV) by Brazilian and Peruvian antivenoms was tested. The results of this study increase the scarce knowledge about PCdV composition and demonstrate antivenom recognition of PCdV proteins, indicating a possible efficiency of these antivenoms to treat Peruvian Crotalus durissus accidents
Project description:Partial genome microarray and plankton cells RNA was isolated from biofilms and from planktonic cells grown in SD media. Samples were labeled with either Cy5 or Cy3. Four independent biological replicates were compared, including dye swaps.
Project description:REEBUS (Environmental sequencing of marine protistan plankton communities reveals the effects of mesoscale cyclonic eddy transport on regional protistan diversity in subtropical offshore waters)
Project description:In this study we applied MASC-seq (massive and parallel microarray sequencing, https://doi.org/10.1038/ncomms13182), a scRNA-seq method that facilitates sequencing of thousands of cells in parallel, and that couples microscope images with the single cell transcriptome data. For this method, fixed cells are spread over a microarray with 100 μm-sized spots of DNA capture probes with spot-specific indices. The cells are first imaged using a scanning microscope and then permeabilized, releasing their RNA out of the cells and bind to the probes on the array. cDNA is synthesized, harvested and sequenced, and, using the spot-specific barcode-sequences, cDNA sequences stemming from a specific spot (i.e., cell) can be linked to the microscope image of the corresponding cell. However, until now, the MASC-seq method has only been applied to mammalian cells. The aim of this study was to test and adapt the MASC-seq method for application on unicellular eukaryotic plankton. We applied and optimized the method on three cultured plankton representatives, abundant in communities of aquatic environments, Phaeodactylum tricornutum (a diatom, silica and polysaccharide cell walls 23), Heterocapsa sp. (a dinoflagellate, cellulose thecal plates 24) and Tetrahymena thermophila (a ciliate, lipid membrane 25) which all have different size and diverse cell surface structures common to plankton. We optimized several steps in the protocol to make it more suitable for planktonic cells and compared the results from MASC-seq generated single cell transcriptomes to bulk RNA sequencing.