Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin
In this study, we present the first spatial transcriptomic atlas of Atlantic salmon skin using the Visium Spatial Gene Expression protocol. We utilized frozen skin tissue from 4 distinct sites, namely the operculum, pectoral and caudal fins, and scaly skin at the flank of the fish close to the later...
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ftpubmed:oai:pubmedcentral.nih.gov:10627282 2023-12-10T09:46:47+01:00 Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin Sveen, Lene R Robinson, Nicholas Krasnov, Aleksei Daniels, Rose Ruiz Vaadal, Marianne Karlsen, Christian Ytteborg, Elisabeth Robledo, Diego Salisbury, Sarah Dagnachew, Binyam Lazado, Carlo C Tengs, Torstein 2023-09-19 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627282/ http://www.ncbi.nlm.nih.gov/pubmed/37724757 https://doi.org/10.1093/g3journal/jkad215 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627282/ http://www.ncbi.nlm.nih.gov/pubmed/37724757 http://dx.doi.org/10.1093/g3journal/jkad215 © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. G3 (Bethesda) Investigation Text 2023 ftpubmed https://doi.org/10.1093/g3journal/jkad215 2023-11-12T01:47:42Z In this study, we present the first spatial transcriptomic atlas of Atlantic salmon skin using the Visium Spatial Gene Expression protocol. We utilized frozen skin tissue from 4 distinct sites, namely the operculum, pectoral and caudal fins, and scaly skin at the flank of the fish close to the lateral line, obtained from 2 Atlantic salmon (150 g). High-quality frozen tissue sections were obtained by embedding tissue in optimal cutting temperature media prior to freezing and sectioning. Further, we generated libraries and spatial transcriptomic maps, achieving a minimum of 80 million reads per sample with mapping efficiencies ranging from 79.3 to 89.4%. Our analysis revealed the detection of over 80,000 transcripts and nearly 30,000 genes in each sample. Among the tissue types observed in the skin, the epithelial tissues exhibited the highest number of transcripts (unique molecular identifier counts), followed by muscle tissue, loose and fibrous connective tissue, and bone. Notably, the widest nodes in the transcriptome network were shared among the epithelial clusters, while dermal tissues showed less consistency, which is likely attributable to the presence of multiple cell types at different body locations. Additionally, we identified collagen type 1 as the most prominent gene family in the skin, while keratins were found to be abundant in the epithelial tissue. Furthermore, we successfully identified gene markers specific to epithelial tissue, bone, and mesenchyme. To validate their expression patterns, we conducted a meta-analysis of the microarray database, which confirmed high expression levels of these markers in mucosal organs, skin, gills, and the olfactory rosette. Text Atlantic salmon Salmo salar PubMed Central (PMC) G3: Genes, Genomes, Genetics 13 11 |
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Investigation Sveen, Lene R Robinson, Nicholas Krasnov, Aleksei Daniels, Rose Ruiz Vaadal, Marianne Karlsen, Christian Ytteborg, Elisabeth Robledo, Diego Salisbury, Sarah Dagnachew, Binyam Lazado, Carlo C Tengs, Torstein Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin |
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Investigation |
description |
In this study, we present the first spatial transcriptomic atlas of Atlantic salmon skin using the Visium Spatial Gene Expression protocol. We utilized frozen skin tissue from 4 distinct sites, namely the operculum, pectoral and caudal fins, and scaly skin at the flank of the fish close to the lateral line, obtained from 2 Atlantic salmon (150 g). High-quality frozen tissue sections were obtained by embedding tissue in optimal cutting temperature media prior to freezing and sectioning. Further, we generated libraries and spatial transcriptomic maps, achieving a minimum of 80 million reads per sample with mapping efficiencies ranging from 79.3 to 89.4%. Our analysis revealed the detection of over 80,000 transcripts and nearly 30,000 genes in each sample. Among the tissue types observed in the skin, the epithelial tissues exhibited the highest number of transcripts (unique molecular identifier counts), followed by muscle tissue, loose and fibrous connective tissue, and bone. Notably, the widest nodes in the transcriptome network were shared among the epithelial clusters, while dermal tissues showed less consistency, which is likely attributable to the presence of multiple cell types at different body locations. Additionally, we identified collagen type 1 as the most prominent gene family in the skin, while keratins were found to be abundant in the epithelial tissue. Furthermore, we successfully identified gene markers specific to epithelial tissue, bone, and mesenchyme. To validate their expression patterns, we conducted a meta-analysis of the microarray database, which confirmed high expression levels of these markers in mucosal organs, skin, gills, and the olfactory rosette. |
format |
Text |
author |
Sveen, Lene R Robinson, Nicholas Krasnov, Aleksei Daniels, Rose Ruiz Vaadal, Marianne Karlsen, Christian Ytteborg, Elisabeth Robledo, Diego Salisbury, Sarah Dagnachew, Binyam Lazado, Carlo C Tengs, Torstein |
author_facet |
Sveen, Lene R Robinson, Nicholas Krasnov, Aleksei Daniels, Rose Ruiz Vaadal, Marianne Karlsen, Christian Ytteborg, Elisabeth Robledo, Diego Salisbury, Sarah Dagnachew, Binyam Lazado, Carlo C Tengs, Torstein |
author_sort |
Sveen, Lene R |
title |
Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin |
title_short |
Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin |
title_full |
Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin |
title_fullStr |
Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin |
title_full_unstemmed |
Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin |
title_sort |
transcriptomic landscape of atlantic salmon (salmo salar l.) skin |
publisher |
Oxford University Press |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627282/ http://www.ncbi.nlm.nih.gov/pubmed/37724757 https://doi.org/10.1093/g3journal/jkad215 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
G3 (Bethesda) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627282/ http://www.ncbi.nlm.nih.gov/pubmed/37724757 http://dx.doi.org/10.1093/g3journal/jkad215 |
op_rights |
© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_doi |
https://doi.org/10.1093/g3journal/jkad215 |
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G3: Genes, Genomes, Genetics |
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13 |
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11 |
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1784890286219984896 |