Ontology highlight
ABSTRACT:
PROVIDER: PRJNA431078 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas Samples of 38 developmental stages from egg to juvenile were analyzed using single-end 49 bp RNA-seq. Two libraries mixed by RNAs from different developmental stages were analyzed using paired-end 90 bp RNA-seq. A total of 11 samples mainly from 8 organs (mantle, gill,adductor muscle, digestive gland, hemocyte, labial palp, female gonad and male gonad) were analyzed using paired-end 90 bp RNA-seq. At the same time, single-end 49 bp RNA-seq was conducted on 61 samples collected from adult oysters subjected to 9 types of environmental stressors (exposure to air, salinity, temperature, and exposure to metals).
2012-09-13 | E-GEOD-31012 | 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: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:Research using the oyster Crassostrea gigas as a model has experienced a rapid growth in recent years thanks to the development of high throughput molecular technologies. As many as 56,268 EST sequences have so far been sequenced, representing a genome-wide resource that can be used for microarray investigations. We have developed an oyster microarray containing cDNAs representing 31,918 unique transcribed sequences. The genes spotted on the array have been selected from the publicly accessible GigasDatabase established from cDNA libraries derived from a wide variety of tissues and different developmental stages. n this paper, we report the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglion, hemocytes, labial palps and digestive gland. Following validation of the microarray, statistical analyses were used to identify genes differentially expressed among tissues and define clusters of tissue-specific genes. These genes reflect well major tissue-specific functions at the molecular level. Analysis of hierarchical clustering data also predicted the involvement of un-annotated genes in selected functional pathways. In a second instance, microarray data were used to accurately select housekeeping genes common to all tissues. Their expression profiles was compared to common oyster standard genes used for quantitative RT-PCR calibration (actin, g3apdh and ef1α). The novel candidate housekeeping gene, adp-ribosylation factor 1 (arf1) and g3apdh gene seem to be more robust for normalizing gene expression data of tissues. This study provides a new source for annotating the oyster genome. It also identified new candidate housekeeping genes, a prerequisite for accurate quantitative RT-PCR expression profiling. Gene expression was measured in 9 tissues: Female gonad, male gonad, mantle, gills, posterior adductor muscle, visceral ganglion, hemocytes, labial palps, digestive gland.Three to four biological replicates were analysed per tissue. These were from distinct animals for female gonad, male gonad, mantle, gills, posterior adductor muscle, labial palps and digestive glands, or obtained from a pool of 6 individuals for hemocytes and visceral ganglion.
2011-10-15 | E-GEOD-26265 | 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: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: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: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