Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12689512_1.fastq.gz | Fastqsanger.gz | |||
| SRR12689512_2.fastq.gz | Fastqsanger.gz | |||
| SRR12689513_1.fastq.gz | Fastqsanger.gz | |||
| SRR12689513_2.fastq.gz | Fastqsanger.gz | |||
| SRR12689514_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The aim of this study was to RNA-sequencing (RNA-seq) to investigate further the gill transcriptome during the early stage of infection, prior to the appearance of mucoid lesions on the gills of amoebic gill disease (ADG)-affected fish. Methods: This study investigated the gill transcriptomic profile of pre-clinical AGD using RNA-sequencing (RNA-seq) technology. RNA-seq libraries generated at 0, 4, 7, 14 and 16 days post inoculation (dpi) RNA-seq data was validated using real-time, quantitative PCR (qPCR) analysis. Results: This study identified 29,357 Differentially Expressed Genes (DEGs) over the course of 16 days follwing exposure to N.perurans , the caustative agent of Amoebic gill disease. With many genes differentially regualted at more tehn one time point, the number of individual gene identified as down-regulated was 8,524 and up-regulated was 10,826. DEGs mapped to 224 Gene Ontology (GO) terms, 27 reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and 15 Reactome Gene Sets. Conclusions:Molecular diagnostics and histopathology, but not gill scores, provided an accurate record of disease progression during early stage onset of AGD, prior to evidence of clinical signs on the gill. At 7 days post infection (dpi), there was evidence of innate immune response activation and a concomitant immune suppression involving signalling pathways for cytokines, specifically interleukins.
2021-07-13 | GSE179972 | GEO
Project description:The experiment focused on the transcriptomic changes associated with gill inflammation in sea farmed Atlantic salmon (Salmo salar). To ensure the multifactorial aspect of gill inflammation, fish were sampled at three marine production sites (A on Isle of Mull, B in Shetland and C in Shetland) between October 2017 and March 2018. All fish were of strain Fanad and originated from the same egg fertilisation batch. They were reared in different hatcheries (Couldoran, Pettigo-Damph and Knock-Frisa for sites A, B and C, respectively) for one year and entered the sea in spring 2017. The resultant gill tissues (44 samples in total with 1 gill sample per fish) were first scored for proliferative gill disease (PGD), using gross morphology PGD scores from 0 with no visual pathology to 5 with severe visual pathology, and then subjected to RNA-seq and histopathological (microscopic) examination. One RNA-seq sample (fish 95) was identified as an outlier and removed from the subsequent analysis. As a result, the analysis aiming to integrate gill transcriptome, gross morphology and histopathology was performed on 43 gill samples, classified either as PGD score 1 (n = 26) or PGD score 3 (n = 17). In total, 20 gill samples originated from site A (10 with PGD1 and 10 with PGD 3, 10 samples from site B (7 with PGD1 and 3 with PGD 3) and 13 samples from site C (9 with PGD1 and 4 with PGD 3).
2020-06-01 | E-MTAB-8855 | biostudies-arrayexpress
Project description:Whereas the gill chambers of extant jawless vertebrates (lampreys and hagfish) open directly into the environment, jawed vertebrates have evolved skeletal appendages that promote the unidirectional flow of oxygenated water over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single operculum covering a large common gill cavity in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here we find that these divergent gill cover patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs, and we identify a deeply conserved Pou3f3 arch enhancer that is present in nearly all jawed vertebrates but undetectable in lampreys. Despite only minor sequence differences, bony fish and cartilaginous fish versions of this enhancer are sufficient to drive the respective single versus multiple gill arch expression. In zebrafish, loss of Pou3f3 gene function or its conserved enhancer disrupts gill cover formation. Conversely, forced expression of Pou3f3b in the gill arches generates ectopic skeletal elements reminiscent of the multiple gill covers of cartilaginous fish. Emergence and modification of this ancient Pou3f3 enhancer may thus have contributed to the acquisition and diversification of gill covers during early gnathostome evolution.
2020-06-17 | GSE140636 | GEO
Project description:In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine, we isolated endoderm-derived GFP+ cells and remaining DsRedx+ cells (hematopoiesis-derived macrophages) from the gill (sox17_gill_GFP, sox17_gill_DsRedx) and intestine (sox17_intestine_GFP, sox17_intestine_DsRedx) of 4-OHT treated Tg(sox17:CreERT2;mpeg1:loxP-DsRedx-loxP-GFP) fish and performed RNA-seq. Both T-SNE analysis and feature gene comparison indicate that the endoderm-derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm-derived mpeg1+ cells as metaphocytes.
2020-11-24 | GSE155287 | GEO
Project description:Animal mucosal barriers constantly interact with the external environment and this interaction is markedly different in aquatic and terrestrial environments. Transitioning from water to land was a critical step in vertebrate evolution but the immune adaptations that mucosal barriers such as the skin underwent during that process are essentially unknown. Vertebrate animals such as the African lungfish have a bimodal life, switching from freshwater to terrestrial habitats when environmental conditions are not favorable. African lungfish skin mucus secretions contribute to the terrestrialization process by forming a cocoon that surrounds and protect the lungfish body. The goal of this study is to characterize the skin mucus immunoproteome of African lungfish, Protopterus dolloi, before and during the induction phase of terrestrialization as well as the immunoproteome of the gill mucus during the terrestrialization induction phase. Using LC-MS/MS, we identified a total of a total of 974 proteins using a lungfish Illumina RNA-seq database and 880 proteins using a lungfish 454 RNA-seq database for annotation in the three samples analyzed (control skin mucus, terrestrialized skin mucus and terrestrialized gill mucus). The terrestrialized skin mucus proteome was enriched in proteins with known antimicrobial functions such as histones and S100 proteins. In support, gene ontology analyses showed that the terrestrialized skin mucus proteome has predicted functions in processes such as viral process, defense response to Gram negative bacterium and tumor necrosis factor mediated signaling. Importantly, we observed a switch in immunoglobulin heavy chain secretion upon terrestrialization, with IgW1L and IgM1 present in control skin mucus and IgW1L, IgM1 and IgM2 in terrestrialized skin mucus. Combined, these results indicate an increase investment in the production of unique immune molecules in P. dolloi skin mucus in response to terrestrialization that likely better protect lungfish against external aggressors found in land.
2018-10-19 | PXD008981 | Pride