Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX

The gill of teleost fish is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its extensive interface with the environment, the gill plays a key role as a primary mucosal d...

Full description

Bibliographic Details
Main Authors: Elżbieta Król (3510458), Patricia Noguera (3966809), Sophie Shaw (8994098), Eoin Costelloe (8994101), Karina Gajardo (1614955), Victoria Valdenegro (305163), Ralph Bickerdike (3612866), Alex Douglas (527078), Samuel A. M. Martin (8994104)
Format: Dataset
Language:unknown
Published: 2020
Subjects:
Online Access:https://doi.org/10.3389/fgene.2020.00610.s004
id ftpurdueuniv:oai:figshare.com:article/12511946
record_format openpolar
spelling ftpurdueuniv:oai:figshare.com:article/12511946 2023-05-15T15:31:38+02:00 Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX Elżbieta Król (3510458) Patricia Noguera (3966809) Sophie Shaw (8994098) Eoin Costelloe (8994101) Karina Gajardo (1614955) Victoria Valdenegro (305163) Ralph Bickerdike (3612866) Alex Douglas (527078) Samuel A. M. Martin (8994104) 2020-06-19T04:18:20Z https://doi.org/10.3389/fgene.2020.00610.s004 unknown https://figshare.com/articles/Table_10_Integration_of_Transcriptome_Gross_Morphology_and_Histopathology_in_the_Gill_of_Sea_Farmed_Atlantic_Salmon_Salmo_salar_Lessons_From_Multi-Site_Sampling_XLSX/12511946 doi:10.3389/fgene.2020.00610.s004 CC BY 4.0 CC-BY Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy proliferative gill disease gene expression RNA-seq immune response gill inflammation aquaculture climate change Dataset 2020 ftpurdueuniv https://doi.org/10.3389/fgene.2020.00610.s004 2020-06-25T10:25:09Z The gill of teleost fish is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its extensive interface with the environment, the gill plays a key role as a primary mucosal defense tissue against pathogens, as manifested by the presence of the gill-associated lymphoid tissue (GIALT). In recent years, the prevalence of multifactorial gill pathologies has increased significantly, causing substantial losses in Atlantic salmon aquaculture. The transition from healthy to unhealthy gill phenotypes and the progression of multifactorial gill pathologies, such as proliferative gill disease (PGD), proliferative gill inflammation (PGI) and complex gill disorder (CGD), are commonly characterized by epithelial hyperplasia, lamellar fusion and inflammation. Routine monitoring for PGD relies on visual inspection and non-invasive scoring of the gill tissue (gross morphology), coupled with histopathological examination of gill sections. To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). Our results strongly suggested that the changes in PGD scores of the gill tissue were not associated with the changes in gene expression or histopathology. In contrast, integration of the gill RNA-seq data with the gill histopathology enabled us to identify common gene expression patterns associated with multifactorial gill disease, independently from the origin of samples. We demonstrated that the gene expression patterns associated with multifactorial gill disease were dominated by two processes: a range of immune responses driven by pro-inflammatory cytokines and the events associated with tissue damage and repair, driven by caspases and angiogenin. Dataset Atlantic salmon Salmo salar Purdue University: e-Pubs
institution Open Polar
collection Purdue University: e-Pubs
op_collection_id ftpurdueuniv
language unknown
topic Genetics
Genetic Engineering
Biomarkers
Developmental Genetics (incl. Sex Determination)
Epigenetics (incl. Genome Methylation and Epigenomics)
Gene Expression (incl. Microarray and other genome-wide approaches)
Genome Structure and Regulation
Genomics
Genetically Modified Animals
Livestock Cloning
Gene and Molecular Therapy
proliferative gill disease
gene expression
RNA-seq
immune response
gill inflammation
aquaculture
climate change
spellingShingle Genetics
Genetic Engineering
Biomarkers
Developmental Genetics (incl. Sex Determination)
Epigenetics (incl. Genome Methylation and Epigenomics)
Gene Expression (incl. Microarray and other genome-wide approaches)
Genome Structure and Regulation
Genomics
Genetically Modified Animals
Livestock Cloning
Gene and Molecular Therapy
proliferative gill disease
gene expression
RNA-seq
immune response
gill inflammation
aquaculture
climate change
Elżbieta Król (3510458)
Patricia Noguera (3966809)
Sophie Shaw (8994098)
Eoin Costelloe (8994101)
Karina Gajardo (1614955)
Victoria Valdenegro (305163)
Ralph Bickerdike (3612866)
Alex Douglas (527078)
Samuel A. M. Martin (8994104)
Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX
topic_facet Genetics
Genetic Engineering
Biomarkers
Developmental Genetics (incl. Sex Determination)
Epigenetics (incl. Genome Methylation and Epigenomics)
Gene Expression (incl. Microarray and other genome-wide approaches)
Genome Structure and Regulation
Genomics
Genetically Modified Animals
Livestock Cloning
Gene and Molecular Therapy
proliferative gill disease
gene expression
RNA-seq
immune response
gill inflammation
aquaculture
climate change
description The gill of teleost fish is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its extensive interface with the environment, the gill plays a key role as a primary mucosal defense tissue against pathogens, as manifested by the presence of the gill-associated lymphoid tissue (GIALT). In recent years, the prevalence of multifactorial gill pathologies has increased significantly, causing substantial losses in Atlantic salmon aquaculture. The transition from healthy to unhealthy gill phenotypes and the progression of multifactorial gill pathologies, such as proliferative gill disease (PGD), proliferative gill inflammation (PGI) and complex gill disorder (CGD), are commonly characterized by epithelial hyperplasia, lamellar fusion and inflammation. Routine monitoring for PGD relies on visual inspection and non-invasive scoring of the gill tissue (gross morphology), coupled with histopathological examination of gill sections. To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). Our results strongly suggested that the changes in PGD scores of the gill tissue were not associated with the changes in gene expression or histopathology. In contrast, integration of the gill RNA-seq data with the gill histopathology enabled us to identify common gene expression patterns associated with multifactorial gill disease, independently from the origin of samples. We demonstrated that the gene expression patterns associated with multifactorial gill disease were dominated by two processes: a range of immune responses driven by pro-inflammatory cytokines and the events associated with tissue damage and repair, driven by caspases and angiogenin.
format Dataset
author Elżbieta Król (3510458)
Patricia Noguera (3966809)
Sophie Shaw (8994098)
Eoin Costelloe (8994101)
Karina Gajardo (1614955)
Victoria Valdenegro (305163)
Ralph Bickerdike (3612866)
Alex Douglas (527078)
Samuel A. M. Martin (8994104)
author_facet Elżbieta Król (3510458)
Patricia Noguera (3966809)
Sophie Shaw (8994098)
Eoin Costelloe (8994101)
Karina Gajardo (1614955)
Victoria Valdenegro (305163)
Ralph Bickerdike (3612866)
Alex Douglas (527078)
Samuel A. M. Martin (8994104)
author_sort Elżbieta Król (3510458)
title Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX
title_short Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX
title_full Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX
title_fullStr Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX
title_full_unstemmed Table_10_Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.XLSX
title_sort table_10_integration of transcriptome, gross morphology and histopathology in the gill of sea farmed atlantic salmon (salmo salar): lessons from multi-site sampling.xlsx
publishDate 2020
url https://doi.org/10.3389/fgene.2020.00610.s004
genre Atlantic salmon
Salmo salar
genre_facet Atlantic salmon
Salmo salar
op_relation https://figshare.com/articles/Table_10_Integration_of_Transcriptome_Gross_Morphology_and_Histopathology_in_the_Gill_of_Sea_Farmed_Atlantic_Salmon_Salmo_salar_Lessons_From_Multi-Site_Sampling_XLSX/12511946
doi:10.3389/fgene.2020.00610.s004
op_rights CC BY 4.0
op_rightsnorm CC-BY
op_doi https://doi.org/10.3389/fgene.2020.00610.s004
_version_ 1766362159425519616