Oyster hemolymph microbiota - experimental data
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Project description:Deep sequencing of mRNA from Pacific oyster Crassostrea gigas
2014-07-26 | GSE31011 | GEO
Project description:miRNA sequencing of Pacific oyster Crassostrea gigas for different organs and developmental stages.
2014-07-26 | GSE31009 | GEO
Project description:Deep sequencing of mRNA from Pacific oyster Crassostrea gigas Competent larvae of Crassostrea gigas were treated with epinephrine solution, and then sampled at different time intervals. For shell damage experiment, shell were broken and then tissues were sampled at different time intervals.
2014-07-26 | E-GEOD-31011 | biostudies-arrayexpress
Project description:Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas
2012-09-13 | GSE31012 | GEO
Project description:Marine intertidal organisms commonly face hypoxic stress during low tide emersion; moreover, eutrophic conditions and sediment nearness could lead to hypoxic phenomena; it is indeed important to understand the molecular processes involved in the response to hypoxia. In this study the molecular response of the Pacific oyster Crassostrea gigas to prolonged hypoxia (2 mg O2 L-1 for 20 d) was investigated under experimental conditions. A transcriptomic approach was employed using a cDNA microarray of 9058 C. gigas clones to highlight the genetic expression patterns of the Pacific oyster under hypoxic conditions. Lines of oysters resistant (R) and susceptible (S) to summer mortality were used in this study. This is the first study employing microarrays to characterize the genetic markers and metabolic pathways responding to hypoxic stress in C. gigas.
2010-09-01 | GSE23883 | GEO
Project description:Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably in Northern Europe. To explore adaptation on reproductive traits of population considered as invasive, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark. A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several genes differentially expressed between the Danish and French progenies, and with an intermediate expression level in hybrids (additive behavior). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism known to be implicated in coordinated control of reproduction. Our results suggest adaptation of invasive populations during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, fertility and gamete quality. A common garden experiment was performed in order to compare progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Progenies were reared under standard hatchery and nursery conditions until gonadal maturation. The employed arrays were Agilent 60-mer 4x44K custom microarrays, containing 31,918 C. gigas ESTs, designed by Dheilly et al. (2011).
2015-02-20 | E-GEOD-66103 | biostudies-arrayexpress
Project description:Ostreid Herpesvirus type 1 (OsHV-1) has become a serious infective agent of the Pacific oyster livestock worldwide. In particular, the OsHV-1 muVar subtype has been associated to severe mortality episodes concerning Crassostrea gigas in France and other regions of the world such as Australia and New Zealand. Factors triggering productive infections and virus interactions with susceptible and resistant bivalve hosts are not completely understood though some studies have been undertaken to explore the genes expressed in oysters after infection. We took advantage of an highly infected oyster sample to perform an in-vivo dual RNA-seq analysis. An extremely high sequencing coverage allowed us to explore in detail the Herpesvirus genome and transcriptome, and to identify viral-activated molecular pathways in Crassostrea gigas, thus expanding the current knowledge on the host-virus interactions.
2014-12-31 | E-MTAB-2552 | biostudies-arrayexpress
Project description:miRNA sequencing of Pacific oyster Crassostrea gigas for different organs and developmental stages. Two RNA pools were created and sequenced by mixing the samples before and after the developmental stage "D shaped larvae". Then ten developmental samples and eleven samples from 7 organs were sequenced.
2014-07-26 | E-GEOD-31009 | biostudies-arrayexpress
Project description:The Pacific oyster Crassostrea gigas, a commercially important species inhabiting the intertidal zone, can tolerate temperature fluctuations. Heat shock transcription factor 1 (HSF1) plays an important role in the process of resistance of thermal stress. However, HSF1 has not been fully characterized in the Pacific oyster. C. gigas with an expansion of heat shock protein (HSP) 70. In this study, we analyzed genes regulated by HSF1 in response to heat shock by Chromatin immunoprecipitation followed sequencing (ChIP-seq), determined the expression patterns of target genes by qRT-PCR, and validated the regulatory relationship between one HSP70 and HSF1. We found 916 peaks corresponding to specific binding sites of HSF1, and peaks were annotated to nearest genes. In Gene Ontology analysis, HSF1 target genes was related to signal transduction, energy production, and response to biotic stimulus. Four HSP70 genes, two HSP40 genes, and one small HSP gene exhibited binding to HSF1. One HSP70 with a binding site in the promoter region was validated to be regulated by HSF1 under heat shock. These results provide a basis for future studies aimed at determining the mechanisms underlying thermal tolerance and provide insights into gene regulation in the Pacific oyster.
2020-10-16 | GSE138959 | GEO
Project description:The Pacific oyster (Crassostrea gigas) is a kind of marine bivalve of great economic and ecological importance and is among the animals possessing the highest level of genome DNA variations. Despite large efforts made for the discovery of Pacific oyster SNPs in many research groups, challenge still remains as how to utilize SNPs in a high-throughput, transferable and economical manner. In the study, we constructed an oyster 190K SNP array with Affymetrix Axiom genotyping technology. A total of 190,420 SNPs were designed on the chip, which were selected from 54 M SNPs identified by re-sequencing of more than 400 Pacific oysters. Genotyping results from 96 wild oysters indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. Carrying 133K polymorphic SNPs, the oyster 190K SNP array is the first high density SNP chip with the largest throughput currently in mollusc and is commercially available to the worldwide research community.
2017-03-22 | GSE94633 | GEO