Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10671800.fastq.gz | Fastqsanger.gz | |||
| SRR10671801.fastq.gz | Fastqsanger.gz | |||
| SRR10671802.fastq.gz | Fastqsanger.gz | |||
| SRR10671803.fastq.gz | Fastqsanger.gz | |||
| SRR10671804.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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.
2021-05-01 | GSE145993 | 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: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
2010-02-04 | E-GEOD-14306 | biostudies-arrayexpress
Project description:This work reports a comprehensive and integrated microstructural, biochemical and proteomics study on the shell matrix of Spondylus gaederopus, the Mediterranean thorny oyster. We investigate the skeletal matrix proteins which are involved in biomineralization and compare the identified Spondylus sequences with other shell proteins, that are publicly available in databases. Using high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) we characterized several shell protein fractions, isolated by different bleaching treatments. We identified six shell proteins, which also displayed features and domains typically found in biomineralized tissues, including the prevalence of intrinsically disordered regions. However, many reconstructed peptide sequences (de novo) could not be matched to any known shell proteins and we suggest that these probably represent lineage-specific sequences. The proteomic data implies that Spondylus may have evolved a distinct molecular toolkit for biomineralization. Using high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) we characterized several shell protein fractions, isolated by different bleaching treatments. Six shell proteins were identified, which displayed features and domains typically found in biomineralized tissues, including the prevalence of intrinsically disordered regions. However, most of the reconstructed peptide sequences (de novo) could not be matched to any known shell proteins and probably represent lineage-specific sequences.
2020-03-31 | PXD016760 | Pride
Project description:Shells of pearl oyster are natural biominerals with remarkable properties and can be repaired after damage, which are regulated by biomacromolcules especially shell matrix proteins (SMPs). Identifying SMPs is critical for further understanding the process. Although proteomic methods have been used to reveal the complex protein mixture in mature shells, the proteomics of repaired shells after shell damage have not been reported before. Here, we studied the SMPs of the repaired shells (prismatic layers) 5-10 days after shell damage in Pinctada fucata by integrating transcriptomics and proteomics and compared the microstructure difference between repaired and mature shells. Although the repaired shells are calcite, similar to mature shells, the microstructure of repaired shells has holes in the center of prisms with irregular and curved edges. In total, we found 49 SMPs from the repaired shells including some proteins only existing in mature nacreous layers. Peroxidase-like protein and beta-N-acetylhexosaminidase may be important players in repaired shells. In addition, they have the capability to affect CaCO3 crystallization process in vitro, altering the packing and reducing the crystallinity of crystals. This study could improve our understanding of shell repair process and lay the foundation for studying SMPs-controlled biomineralization.
2019-03-26 | PXD010130 | Pride
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.
2021-03-28 | GSE107713 | 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