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Transcriptomic characterisation of transitioning cell types in the skin of Atlantic salmon

ABSTRACT: Transcriptomic characterisation of transitioning cell types in the skin of Atlantic salmon

PROVIDER: PRJNA1211063 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32009598.fastq.gz	Fastqsanger.gz
	SRR32009599.fastq.gz	Fastqsanger.gz

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Transcriptomic characterisation of transitioning cell types in the skin of Atlantic salmon

Project description:Background The skin maintains the body’s integrity and serves as the first line of defence against pathogens, stressors and mechanical injuries. Despite the global significance of salmon in aquaculture, how cells transcriptomic profile varies during wound healing, remains unexplored. Teleost contain adult pluripotent cells that differentiate into various tissues, including bone, cartilage, tendon, ligament, adipose, dermis, muscle and connective tissue within the skin. These cells are pivotal for preserving the integrity of skin tissue throughout an organism´s lifespan and actively participate in the wound healing processes. In this study, we characterise the transcriptomic profiles of putative mesenchymal stromal cells (fibroblast-like adult stem cells) in healthy Atlantic salmon tissue and during the wound healing process. Results Single-nucleus sequencing and spatial transcriptomics were used to detect transcriptomic changes occurring during wound healing that are commonly associated with mesenchymal stromal cells. We followed the transcriptomic activity of these cells during an in vivo wound healing time course study showing that these cells become more transcriptionally active during the remodelling stage of wound healing. The changes detected give insights into the potential differentiation pathways leading to osteogenic and fibroblast lineages in the skin of Atlantic salmon. Conclusions We chart the transcriptomic activity of sub-clusters of putative differentiating stromal cells during the process of wound healing for the first time, revealing different spatial niches of the various putative MSC subclusters, and setting the stage for further investigation of the manipulation of transitioning cell types to improve fish health. KEYWORDS: Salmo salar, skin, mesenchymal stromal cells, single-cell sequencing, spatial transcriptomics, wound healing, spatial niche.

2025-01-15 | GSE287051 | GEO

Molecular characterisation of the Atlantic salmon gill epithelial cell line ASG-10

Project description:Fish gills are not only the respiratory organ, but also essential for ion-regulation, acid-base control, detoxification, waste excretion and host defense. Multifactorial gill diseases are common in farmed Atlantic salmon, and still poorly understood. Understanding gill pathophysiology is of paramount importance, but the sacrifice of large numbers of experimental animals for this purpose should be avoided. Therefore, in vitro models, such as cell lines, are urgently required to replace fish trials. An Atlantic salmon gill epithelial cell line, ASG-10, was established at the Norwegian Veterinary institute in 2018. This cell line forms a monolayer expressing cytokeratin, e-cadherin and desmosomes, hallmarks of a functional epithelial barrier. To determine the value of ASG-10 for comparative studies of gill functions, the characterization of ASG-10 was taken one step further by performing functional assays and comparing the cell proteome and transcriptome with those of gills from juvenile freshwater Atlantic salmon. The ASG-10 cell line appear to be a homogenous cell line consisting of epithelial cells, which express tight junction proteins. We demonstrated that ASG-10 forms a barrier, both alone and in co-culture with the Atlantic salmon gill fibroblast cell line ASG- 13. ASG-10 cells can phagocytose and express several ATP-binding cassette transport proteins. Additionally, ASG-10 expresses genes involved in biotransformation of xenobiotics and immune responses. Taken together, this study provides an overview of functions that can be studied using ASG-10, which will be an important contribution to in vitro gill epithelial research of Atlantic salmon.

2024-01-26 | PXD044533 | Pride

Atlantic salmon

Project description:Atlantic salmon Metagenome

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Atlantic salmon gastric mucosa LC-MSMS

Project description:The Atlantic salmon (Salmo salar) genome contains 10 chitinase encoding genes, but little is known about the function of these chitinases. Three of the chitinase genes have previously been shown to be expressed in the stomach tissue of Atlantic salmon. In the current study we show that the protein products of these genes, the family 18 glycoside hydrolase (GH18) chitinases, Chia.3, Chia.4 and Chia.7 are secreted into the stomach mucosa and are amongst the most abundant proteins in this matrix.

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Project description:This SuperSeries is composed of the following subset Series: GSE26981: Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in skin of Atlantic salmon GSE26984: Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in spleen of Atlantic salmon Refer to individual Series

2011-02-03 | E-GEOD-27013 | biostudies-arrayexpress

Conservation genomics of Atlantic salmon

Project description:This SuperSeries is composed of the following subset Series: GSE19111: Conservation genomics of Atlantic salmon (Year One) GSE19119: Conservation genomics of Atlantic salmon (Year Two) Refer to individual Series

2010-05-19 | E-GEOD-19170 | biostudies-arrayexpress

Atlantic salmon commensal

Project description:Atlantic salmon commensal

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single nuclei RNAseq data from Atlantic salmon (Salmo salar) gill

Project description:An snRNAseq analysis of the Atlantic salmon gill to characterise its cellular complexity and development.

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