Project description:This SuperSeries is composed of the following subset Series: GSE13980: Analysis of the global gene expression profile for pearl oyster, Pinctada maxima, exposed to organotin (tributyltin) GSE14303: Differential expression analysis of genes from the mantle tissue of pearl oyster: Pinctada maxima GSE14305: The microstructural, mineralogical and transcriptional developments of shell biomineralization of Pinctada maxima Refer to individual Series
Project description:To elucidate the modulatory participation of miRNAs in mollusk biomineralization, we have employed high-throughput sequencing to identify miRNAs of pearl oyster, Pinctada fucata. Our study focused on the miRNA expression profile of the mantle, an organ responsible for shell formation of the oyster. The pearl oysters were cultured in the tank with the maintaining conditions of temperature 19 ℃, PH 8.1 and salinity 33‰ in recirculating seawater.
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.
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.
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.
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.
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.
2011-10-16 | GSE26265 | GEO
Project description:Pacific oyster shell color strain mantle
Project description:Hox and ParaHox genes encode transcription factors with conserved similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. We thus conducted experiments to show that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is also a direct target of Pdx in the Pacific oyster. We report that oyster has a diversity of insulin-related genes including one co-expressed with Pdx in the endodermal layer of oyster digestive tissue. Transcriptome analysis reveals functional similarity of this tissue to vertebrate pancreas. Using ATAC-seq we identify a Pdx homeodomain binding site upstream of the endodermally-expressed oyster insulin-related gene and using cell culture demonstrate that oyster Pdx acts as a transcriptional activator through this site. These data argue that a classic homeodomain-target gene interaction dates back to the base of Bilateria.