Ontology highlight
ABSTRACT:
PROVIDER: PRJNA342927 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5152122_1.fastq.gz | Fastqsanger.gz | |||
| SRR5152122_2.fastq.gz | Fastqsanger.gz | |||
| SRR5527414_1.fastq.gz | Fastqsanger.gz | |||
| SRR5527414_2.fastq.gz | Fastqsanger.gz | |||
| SRR5527415_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the full transcriptome (RNA-Seq) of Vibrio fischeri ES114 in rich medium, seawater, and after venting from the Hawaiian bobtail squid Euprymna scolopes. We also report the effects of ribodepletion on low-biomass samples, down to input amount of 1ng total RNA.
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Project description:Sepioloidea lineolata, the striped pyjama squid (family Sepiadariidae), is a small species of benthic squid distributed along the Southern Indo-Pacific coast of Australia. All sepiadariid squids are known to secrete large volumes of viscous slime when stressed. The proteome of S. lineolata slime was analysed by combining high resolution mass spectrometry data with an S. lineolata transcriptome assembled from five tissues including slime. The composition of S. lineolata slime was also compared to that of the closely related S. austrinum (southern bottletail squid). Of the 550 protein groups identified in S. lineolata slime, 321 had orthologs in S. austrinum, and the abundance of these (iBAQ) was highly correlated between species. Both slimes were dominated by a small number of highly abundant proteins and several of these were short secreted proteins that had no homologues outside the class Cephalopoda. The extent of N-glycosylation in the slime of S. lineolata was also studied via glycan cleavage with PNGase-F. Four proteins had strong evidence of N-glycosylated, with treatment with PNGase-F showing a slight increase in peptide identification rates.
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Project description:The marine bacterium Vibrio fischeri requires flagellar motility to undergo symbiotic initiation with its host, the Hawaiian bobtail squid Euprymna scolopes. We sought to identify the genes activated by the sigma54-dependent flagellar master regulator, FlrA, in V. fischeri, thereby determining the flagellar regulon in this model symbiont.
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Project description:Bigfin Reef Squid Metagenomic assembly
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Project description:The light-organ symbiosis between the squid Euprymna scolopes and the luminous bacterium Vibrio fischeri offers the opportunity to decipher the hour-by-hour events that occur during the natural colonization of an animal's epithelial surface by its microbial partners. To determine the genetic basis of these events, a glass-slide microarray was used to characterize the light-organ transcriptome of juvenile squid in response to the initiation of symbiosis. Patterns of gene expression were compared between animals not exposed to the symbiont, exposed to the wild-type symbiont, or exposed to a mutant symbiont defective in either of two key characters of this association: bacterial luminescence or autoinducer (AI) production. Hundreds of genes were differentially regulated as a result of symbiosis initiation, and a hierarchy existed in the magnitude of the host's response to three symbiont features: bacterial presence > luminescence > AI production. Putative host receptors for bacterial surface molecules known to induce squid development are up-regulated by symbiont light production, suggesting that bioluminescence plays a key role in preparing the host for bacteria-induced development. Further, because the transcriptional response of tissues exposed to AI in the natural context (i.e., with the symbionts) differed from that to AI alone, the presence of the bacteria potentiates the role of quorum signals in symbiosis. Comparison of these microarray data with those from other symbioses, such as germ-free/conventionalized mice and zebrafish, revealed a set of shared genes that may represent a core set of ancient host responses conserved throughout animal evolution. Six experimental treatments of juvenile animals were performed for the microarray matrix: uncolonized (Apo); uncolonized, but supplemented with AI (Apo + AI); colonized by wild-type V. fischeri (wild type); colonized by a mutant defective in luciferase synthesis (luxA); colonized by a mutant defective in AI synthesis (luxI); and, colonized by the luxI mutant, but supplemented with AI (luxI + AI). At 18 h postinoculation, animals were anesthetized in 2% ethanol in HOSW, and the light organs were removed into RNAlater (Ambion Biosystems).
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