Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1018915 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26108005_1.fastq.gz | Fastqsanger.gz | |||
| SRR26108005_2.fastq.gz | Fastqsanger.gz | |||
| SRR26108006_1.fastq.gz | Fastqsanger.gz | |||
| SRR26108006_2.fastq.gz | Fastqsanger.gz | |||
| SRR26108007_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:In order to screen and identify biomineralization gene, microarray technique was used to reveal tissues specific expression genes in the brunet mantle edge (ME), mantle centre (MC), and both ME and MC (ME-MC) from assembled transcriptome contigs of Pinctada fucata martensii, ideal pearl oyster for the study of biomineralization. Tissues of ME, MC, hepatopancreas, foot, gill, adductor muscle, heart and intestine were sampled from two females and one male pearl oyster. Gonad was sampled from above three individuals and another two male and one female. Equal amount RNA of each individual hepatopancreas, foot, gill, adductor muscle, heart and intestine were mixed as a composite viscera sample (CV), and equal amount gonad RNA from one male and one female were combined together as a gonad sample (GS). Hybridizations were performed with twelve samples of ME, MC, CV and GS. Gene expression in ME, MC, gonad and other tissues were measured. Gonads were sampled from 6 individuals, and other tissues were sampled from above three individuals.
2016-07-01 | E-GEOD-70439 | biostudies-arrayexpress
Project description:The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden.
2016-06-30 | GSE65653 | GEO
Project description:In order to screen and identify biomineralization gene, microarray technique was used to reveal tissues specific expression genes in the brunet mantle edge (ME), mantle centre (MC), and both ME and MC (ME-MC) from assembled transcriptome contigs of Pinctada fucata martensii, ideal pearl oyster for the study of biomineralization. Tissues of ME, MC, hepatopancreas, foot, gill, adductor muscle, heart and intestine were sampled from two females and one male pearl oyster. Gonad was sampled from above three individuals and another two male and one female. Equal amount RNA of each individual hepatopancreas, foot, gill, adductor muscle, heart and intestine were mixed as a composite viscera sample (CV), and equal amount gonad RNA from one male and one female were combined together as a gonad sample (GS). Hybridizations were performed with twelve samples of ME, MC, CV and GS.
2016-07-01 | GSE70439 | GEO
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:We performed transcriptime analysis (RNA-seq) in the stony coral Crassostrea virginica treated with different nucleotide messengers produced by cGLRs.
2023-06-27 | GSE232087 | GEO
Project description:Background The Pacific oyster Crassostrea gigas (Mollusca, Lophotrochozoa) is an alternative and irregular protandrous hermaphrodite. Little is known about the genetic and phenotypic bases of sex determinism in oysters, and little more about the molecular pathways regulating reproduction. We have recently developed and validated a microarray containing 31,918 oligomers (Dheilly et al., 2011) representing the oyster transcriptome. The application of this microarray to the study of mollusks gametogenesis should provide a better understanding of the key factors involved in sex differentiation and the regulation of oyster reproduction. Results Expression of the 31,918 ESTs was studied in gonads of oysters cultured along the French Atlantic coasts over a yearly reproductive cycle. Principal component analysis and hierarchical clustering first showed a significant divergence in gene expression patterns of males and females beginning when gonial mitosis started. Early expressed male-specific genes included bindin and female-specific genes included foxL2, a pancreatic lipase related protein, cd63 and vitellogenin. ANOVA analysis of the data further revealed 2482 genes differentially expressed during the course of males and/or females gametogenesis. The expression of 434 genes could be localized in either germ cells or somatic cells of the gonad by comparing the transcriptome of gonads to the transcriptomes of striped oocytes and somatic tissues. Analysis of the annotated genes revealed conserved molecular mechanisms between mollusks and mammals. Genes involved in chromatin condensation, DNA replication and repair, mitosis and meiosis regulation, transcription, translation and apoptosis were expressed in both male and female gonads. Additional lists of genes more specifically involved in either spermatogenesis (meiotic phase, in spermatozoids and mature sperm formation and in flagella structure and movement) or oogenesis (female sex differentiation, transcriptional regulation, cell cycle regulation and oocytes maturation) were also generated. Conclusions Our study provides novel insight into spermatogenesis and oogenesis in an alternative hermaphrodite bivalve, the Pacific oyster C. gigas. We identified genes opening new perspectives for functional studies of the signaling pathways implicated in gonad differentiation and development. Individual gonad oysters were sampled in 3 sites: site 1 = Locmariaquer (Brittany, France), site 2 = Baie des Veys (Normandy, France), and site 3 = Argenton (Brittany, France). 8 undifferentiated stage 0 gonads from site 1 were processed. 4 individuals from site 1 were processed for each gonad developmental stage and sex: stage 1 male, stage 1 female, stage 2 male, stage 2 female, stage 3 male, and stage 3 female. Pools of stage 3 females were prepared with individuals from site 1 and site 2 for biological validation of the results. Striped gonads from stage 3 females were prepared for prediction of gene expression localization.
2012-12-01 | E-GEOD-27955 | biostudies-arrayexpress