Microarray summer mortality insitu oyster
Ontology highlight
ABSTRACT:
ORGANISM(S): Magallana gigas
PROVIDER: GSE16448 | GEO | 2009/08/15
SECONDARY ACCESSION(S): PRJNA116015
REPOSITORIES: GEO
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2010-09-01 | GSE23883 | GEO
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:Summer mortality of Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. A large genetic basis and a high heritability were demonstrated for the observed variation in resistance to summer mortality, which offered the possibility to develop lines of oysters that were resistant (R) or susceptible (S) to summer mortality. Previously, genome-wide expression profiling of R and S oyster gonads highlighted reproduction and antioxidant defense as constitutive pathways that operate differentially between these two lines. Here, we show that signaling in innate immunity also operates differentially between these lines and we postulated that it is at the main origin of their difference of survival in the field. From the already published microarray data, we employed an ANOVA analysis that reveals a specific “immune” profile at the date preceding the mortality. In addition, we conducted a microarray profiling of two other tissues, gills and muscle, that also showed an over-representation of the immune genes (46%) among the selected genes. Eleven genes were pinpointed to be simultaneously differentially expressed between R and S lines in the three tissues. Among them, ten are related to “Immune Response”. The kinetics of their mRNA levels appeared clearly different between lines and suggests that in environment, R oysters had the capacity to modulate signaling in innate immunity whereas S oysters did not. This study enhances our understanding of the complex summer mortality syndrome and provides candidates of interest for further functional and genetics studies.
2011-04-22 | GSE25614 | GEO
Project description:Summer mortality of the Pacific oyster Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. Heredity appears to be a major factor determining the sensitivity of oysters to summer mortality, allowing resistant (R) and susceptible (S) lines to be produced. We conducted genome-wide expression profiling of R and S gonads during the 3-month period preceding a summer mortality event using a 9K cDNA microarray that we designed. This transcriptional analysis provides new indications to define markers for Quantitative Trait Loci searches and functional studies, and evaluates the potential role of each gene in the resistance to summer mortality For microarray analysis, R and S oysters were sampled four times (dates 1 to 4: May 9, May 25, June 6, and June 20, respectively). On each date, 3 replicates of 8 oysters were sampled from each line (R and S) and the gonads prepared for total RNA extraction. Furthermore, the entire tissues of 10 wild oysters were collected, pooled and homogenized to constitute a single total RNA sample for use as a reference in all slide hybridizations and RT-PCR analysis. For microarray hybridizations, 5µg of total RNA were directly labeled by reverse transcription and then purified using the Direct ShipShot Labeling kit (Promega). This reaction was performed for each of the 24 gonad samples, with Cy5 (red) incorporation. The reference sample was Cy3-labeled (green) in 24 separate tubes following the same protocol. The 24 Cy3-labeled cDNAs were next pooled, and then divided once more into 24 samples to obtain a homogeneous reference. Equimolar amounts of cDNA samples and cDNA reference labeled with Cy5 and Cy3, respectively, were SpeedVac evaporated and mixed into a single pool with the hybridization buffer (ChipHyb™ hybridization buffer, Ventana Discovery, Tucson, AZ, USA). They were then co-hybridized on the same microarray slide, in a Ventana hybridization station (Ventana Discovery, Tucson, AZ, USA). The data submitted here correspond to the mean of the three replicates for each line and each date, representing 8 samples : gonad_resistant_date1 gonad_sensitive_date1 gonad_resistant_date2 gonad_sensitive_date2 gonad_resistant_date3 gonad_sensitive_date3 gonad_resistant_date4 gonad_sensitive_date4
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2011-11-01 | GSE33390 | GEO
Project description:The cultivated Pacific oyster Crassostrea gigas has suffered for decades large scale summer mortality phenomenon resulting from the interaction between the environment parameters, the oyster physiological and/or genetic status and the presence of pathogenic microorganisms including Vibrio species. To obtain a general picture of the molecular mechanisms implicated in C. gigas immune responsiveness to circumvent Vibrio infections, we have developed the first deep sequencing study of the transcriptome of hemocytes, the immunocompetent cells. Using Digital Gene Expression (DGE), we generated a transcript catalog of up-regulated genes from oysters surviving infection with virulent Vibrio strains (Vibrio splendidus LGP32 and V. aestuarianus LPi 02/41) compared to an avirulent one, V. tasmaniensis LMG 20012(T). For that an original experimental infection protocol was developed in which only animals that were able to survive infections were considered for the DGE approach. We report the identification of cellular and immune functions that characterize the oyster capability to survive pathogenic Vibrio infections. Functional annotations highlight genes related to signal transduction of immune response, cell adhesion and communication as well as cellular processes and defence mechanisms of phagocytosis, actin cytosqueleton reorganization, cell trafficking and autophagy, but also antioxidant and anti-apoptotic reactions. In addition, quantitative PCR analysis reveals the first identification of pathogen-specific signatures in oyster gene regulation, which opens the way for in depth molecular studies of oyster-pathogen interaction and pathogenesis. This work is a prerequisite for the identification of those physiological traits controlling oyster capacity to survive a Vibrio infection and, subsequently, for a better understanding of the phenomenon of summer mortality. 4 Samples.
2011-11-01 | E-GEOD-33390 | biostudies-arrayexpress
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2017-11-20 | E-MTAB-5345 | biostudies-arrayexpress
Project description:Deep sequencing of mRNA from Pacific oyster Crassostrea gigas
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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.
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Project description:miRNA sequencing of Pacific oyster Crassostrea gigas for different organs and developmental stages.
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