Transcriptomic analysis of the body wall of farmed sea cucumber Isostichopus badionotus specimens
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ABSTRACT:
PROVIDER: PRJNA660409 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12552900_1.fastq.gz | Fastqsanger.gz | |||
| SRR12552900_2.fastq.gz | Fastqsanger.gz | |||
| SRR12552901_1.fastq.gz | Fastqsanger.gz | |||
| SRR12552901_2.fastq.gz | Fastqsanger.gz | |||
| SRR12552902_1.fastq.gz | Fastqsanger.gz |
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Project description:These data corresponds to RNA-Seq assays obtained from the body wall of farmed I. badionotus juveniles samples. These raw reads were used to evaluate differential gene expression between wild and farmed Isostichopus badionotus specimens. With this aim, a de-novo transcriptome assembled from wild specimens was used as reference. Further information about de-novo assembled transcriptome is available within the BioProject PRJNA639785.
2020-09-01 | GSE157183 | GEO
Project description:Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.
| S-EPMC8070510 | biostudies-literature
Project description:Gut microbiota of the sea cucumber Isostichopus badionotus
| PRJNA701034 | ENA
Project description:Isostichopus badionotus (de-novo transcriptome assembly and RNA-Seq)
| PRJNA639785 | ENA
Project description:Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disrupts local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic risks posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of late sac fry of a European (EO) farmed (“StofnFiskur”, Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected fewer differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the fitness of wild populations.
2022-03-11 | GSE184425 | GEO
Project description:Structural proteins play critical roles in the food quality, especially texture properties, of sea cucumbers and their products. Most of the previous studies on sea cucumbers focused on few individual proteins, which limited our understanding of how structural proteins influenced the quality of sea cucumbers. Inspired by the clarification of sea cucumber (Apostichopus japonicus) genome, we established an integrated data of structural proteins in the sea cucumber body wall. A portfolio of 2018 structural proteins was screened out from the sea cucumber annotated proteome by bioinformatics analysis. The portfolio was divided into three divisions, including extracellular matrix proteins, muscle proteins, and proteases, and further classified into 18 categories. The presence of 472 proteins in the sea cucumber body wall was confirmed by using a proteomics approach. Moreover, comparative proteomics analysis revealed the spatial distribution heterogeneity of structural proteins in the sea cucumber body wall at a molecular scale. This study suggested that future researches on sea cucumbers could be performed from an integrated perspective, which would reshape the component map of sea cucumber and provide novel insights into the understanding of how the food quality of sea cucumber was determined on a molecular level.
| S-EPMC7599334 | biostudies-literature
Project description:modENCODE_submission_470 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: PD4251 (engineered, target gene myo-3 tagged by GFP); Tissue: body wall muscle; Developmental Stage: Mixed stage of embryos 20dC; Genotype: ccIs4251 [(myo-3::GFP-LacZ) I ; dpy-20(e1282) IV.]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain PD4251 (engineered, target gene myo-3 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue body wall muscle
2010-08-04 | E-GEOD-23260 | biostudies-arrayexpress
Project description:Expression of mutant lamins in human muscle causes muscular dystrophy. We have generated a drosophila model that expresses mutant lamins, modeled after those that cause disease in humans. We used affymetrix microarrays to determine the global changes in gene expression caused by mutant lamins. Dissected 3rd instar larval body wall from transgenic Drosophila expressing either a full length wildtype Lamin C, an N-terminal Lamin C truncation of the first 42 amino acids or a single amino acid substitution in Lamin C at position 489 from a G residue to a V residue under control of the Gal4-UAS. RNA was extracted from 3rd instar larval body wall expressing these mutant Lamin C transgenes and microarray analysis using Affymetrix microarrays.
2015-04-16 | E-GEOD-49959 | biostudies-arrayexpress