Data and information collection on 6 fish skin samples
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Cynoglossus Semilaevis
TISSUE(S): Skin
SUBMITTER: 
Lei Wang
LAB HEAD: Lei Wang
PROVIDER: PXD047789 | Pride | 2024-04-19
REPOSITORIES: Pride
Similar Datasets
Project description:Investigation of expression differences between skin and melanomas from a transgenic BRAFV600E zebrafish model of melanoma The embryos described in this study are further analyzed in a manuscript submitted for publication by White, et al. A 15 chip study using RNA extracted from either WT zebrafish skin, mitf-BRAFV600E;p53-/- skin or mitf-BRAFV600E;p53-/- melanoma
2011-03-30 | E-GEOD-24528 | biostudies-arrayexpress
Project description:The skin mucus of gilthead sea bream was mapped by 1-DE followed by liquid chromatography coupled to high resolution mass spectrometry using a quadrupole time-of-flight mass analyzer. More than 2000 proteins were identified with a protein score filter of 30. The identified proteins were represented in 418 canonical pathways of the Ingenuity Pathway software. After filtering by canonical pathway overlapping, the retained proteins were clustered in three groups. The mitochondrial cluster contained 59 proteins related to oxidative phosphorylation and mitochondrial dysfunction. The second cluster contained 79 proteins related to antigen presentation and protein ubiquitination pathways. The third cluster contained 257 proteins where proteins related to protein synthesis, cellular assembly, and epithelial integrity were over-represented. The latter group also included acute phase response signaling. In parallel, 2-DE methodology identified six proteins spots of different protein abundance when comparing unstressed fish with chronically stressed fish in an experimental model that mimicked daily farming activities. The major changes were associated with a higher abundance of cytokeratin 8 in the skin mucus proteome of stressed fish, which was confirmed by immunoblotting. Overall, these results indicate that skin mucus is a reliable tissue for alternative or complementary stress phenotyping in fish farming.
2018-10-26 | PXD004115 | Pride
Project description:Anopheles gambiae isofemale families from Tororo, Uganda were assayed for resistance to lambda-cyhalothrin (1.5hr exposure). Resistant families were compared to susceptible families. A portion of each family was exposed to 0.05% lambda-cyhalothrin in order to determine the family phenotype. The families used for the array were of known phenotype but were themselves unexposed.
2013-12-03 | E-MTAB-1874 | biostudies-arrayexpress
Project description:Turbot (Scophthalmus maximus) is a valuable resource for aquaculture in Galicia (NW Spain). Since it has been observed that viral hemorraghic septicaemia can affect turbot, among other finfish, increase of knowledge in molecular factors affected by the exposure to pathogen could help to develop strategies of VHSV prevention and treatment. In this study, it has been used a custom oligo-microarray by Agilent to identify genes differentially expressed in several turbot families showing different susceptibility to VHSV. Fishes from each family (n=30) were injected with either VHSV (Resistant) or control medium (Naive) and monitored for 30 days, when each group was splitted in two new groups and rechallenged with VHSV (Infected) or control medium (Control). Gene expression at the head kidney was evaluated, showing than an important proportion of the variation of the gene expression profiles is explained by the genetic background (family). After infection, fish showed an up-regulation of the interferon-induced Mx2 gene, the IL-8 gene and the VHSV-induced protein 5 gene compared with control groups. Familes with high mortality after VHSV infection showed lower levels of expression of molecules secreted in the mucus and, by contrast, higher expression of genes involved in viral entrance into target cells. 4 different families of turbot were subjected to challenged with VHSV and splitted after 30 days in 2
2012-02-14 | E-GEOD-35804 | biostudies-arrayexpress
Project description:Infectious Pancreatic Necrosis (IPN) is a highly contagious birnavirus disease of farmed salmonid fish, which often causes high levels of morbidity and mortality. A large genetic component underlying resistance to this disease has been previously described for Atlantic salmon (Salmo salar L.), which mediates high mortality rates in some families and zero mortality in others. A global comparison of the gene expression profiles of resistant and susceptible Atlantic salmon fry following challenge with the IPN virus was undertaken. Full sibling salmon fry from two IPNV-resistant and two IPNV-susceptible families were challenged with the virus and sampled at 1 day, 7 days and 20 days post-challenge. Significant viral titre was observed in both resistant and susceptible fish at all timepoints, although generally at higher levels in susceptible fish. Microarray interrogations were performed using a custom-designed, oligonucleotide microarray platform (Agilent) with 44 K probes per slide (Salar_2; Agilent Design ID:025520). The design is lodged with ArrayExpress ( under accession number A-MEXP-2065. Dual-label hybridisations were undertaken, with each experimental sample (Cy3 labelled) being competitively hybridised against a pooled reference control (Cy5 labelled) comprising equimolar amounts from each experimental RNA sample. The interrogations comprised 144 separate hybridisations; 2 genotypes (susceptible, resistant) à 2 families for each genotype à 2 challenge states (control, challenged) à 3 timepoints (1, 7, 20 dpi) à 4 biological replicates for resistant (2 from each of two tanks) and 8 biological replicates for susceptible (4 from each of two tanks). A preliminary analysis suggested evidence for a segregating QTL in both the susceptible families and therefore twice as many offspring were screened. It was later established that the evidence for QTL segregation in one of the families was inconclusive and therefore comparisons were made at the family level only. The analyses took the unbalanced design into account.
2016-04-07 | E-MTAB-4275 | biostudies-arrayexpress
Project description:The skin mucus of gilthead sea bream was mapped by 1-DE followed by liquid chromatography coupled to high resolution mass spectrometry using a quadrupole time-of-flight mass analyzer. More than 2000 proteins were identified with a protein score filter of 30. The identified proteins were represented in 418 canonical pathways of the Ingenuity Pathway software. After filtering by canonical pathway overlapping, the retained proteins were clustered in three groups. The mitochondrial cluster contained 59 proteins related to oxidative phosphorylation and mitochondrial dysfunction. The second cluster contained 79 proteins related to antigen presentation and protein ubiquitination pathways. The third cluster contained 257 proteins where proteins related to protein synthesis, cellular assembly, and epithelial integrity were over-represented. The latter group also included acute phase response signaling. In parallel, 2-DE methodology identified six proteins spots of different protein abundance when comparing unstressed fish with chronically stressed fish in an experimental model that mimicked
2018-10-26 | PXD004116 | Pride
Project description:N-3 long chain polyunsaturated fatty acids (n-3LC-PUFA) are essential components of vertebrate membrane lipids and are now at critically low levels in modern Western diets. The main human dietary source for n-3LC-PUFA is fish and seafood, and over 50% of global fish production is currently supplied by aquaculture. However, increasing pressure to include vegetable oils, which are devoid of n-3LC-PUFA, in aquaculture feeds reduces their content in farmed fish flesh. The aim of this investigation was to infer mechanisms determining flesh n-3LC-PUFA content in Atlantic salmon. The TRAITS / SGP Atlantic salmon 17k feature cDNA microarray (ArrayExpress accession: A-MEXP-1790) was used to compare hepatic mRNA expression in 8 families, reared under common conditions, which exhibited contrasting high and low flesh n-3LC-PUFA levels at harvest. The microarray interrogations incorporated a common pooled reference design, comprising a total of 16 hybridisations (8 families x 2 - dye swap). Each family sample comprised RNA pooled from six sibs.
2010-05-01 | E-TABM-955 | biostudies-arrayexpress
Project description:Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the present manuscript the histological and molecular changes underlying skin and scale regeneration in fed and fasted sea bream (Sparus auratus) were studied using a microarray 3 and 7 days after scale removal to provide a comprehensive molecular understanding of the early stages of these processes. Histological analysis of skin/scales revealed 3 days after scale removal re-epithelisation had occurred and the scale pocket had formed. In animals with scales removed, there was significant up-regulation of genes involved in cell cycle regulation, cell proliferation and adhesion, immune response and antioxidant activities. The expression profiles of the fasted animals centred on maintaining energy homeostasis. The utilisation of fasting as a treatment emphasised the competing whole animal physiological requirements with regard to barrier repair, infection control and energy homeostasis. Gene expression of sea bream (Sparus auratus) skin and scales was analysed in normal and treated animals. Three different treatments were applied: 1. scales removal at day 0 of the experiment; 2. unfed fish 7 days prior the start of the experiment; and 3. scales removal at day 0 of the experiment of unfed fish 7 days prior the start of the experiment. Fish were sampled at two different days: day 3 and day 7 after scale removal. Five individuals from control and experimental groups were analysed for both sampling days (3 and 7), resulting in a total of 40 samples analysed by microarray.
2012-01-24 | E-GEOD-30717 | biostudies-arrayexpress
Project description:Anguillid herpesvirus 1 (AngHV) is an important viral pathogen of eel. This study was conducted to investigate the molecular mechanisms and immune response at the protein levels in the skin mucus of AngHV infected Anguilla anguilla. TMT-labelling proteomics with the liquid chromatographytandem mass spectrometry (LC-MS/MS) was used for protein quantitative identification. And the quantitative protein amount was detected by parallel reaction monitoring (PRM) analysis. A total of 3486 proteins were identified, of which 2935 were quantified. When a protein fold change greater than 1.3 or less than 0.76 was considered to indicate a differentially expressed protein (DEP), 187 up-regulated proteins and 126 down-regulated proteins were detected, and most of the DEPs were enriched in CAMs pathway, intestinal immune pathway, herpes simplex virus 1 infection pathway, phagosome pathway and p53 signaling pathway. The results of the DEPs detected by PRM were highly consistent with that of the TMT-labelled quantitative proteomic analysis results.
2023-03-10 | PXD034867 | Pride
Project description:As part of a study investigating the effects of genotype on responses to sustainable feeds in Atlantic salmon, a microarray analysis of the liver transcriptome of two family groups, identified as 'Lean' or 'Fat' (based on flesh lipid content), which were fed a diet containing either 100% fish oil (FO) or 100% vegetable oil (VO) was undertaken. Cholesterol and lipoprotein metabolism pathways that were differentially affected by diet depending on the genetic background of the fish were identified.<br><br>The TRAITS/SGP (v.2.1) salmon 17k cDNA microarray was used in this experiment. A dual-labelled experimental design was employed for the microarray hybridisations. aRNA from each experimental sample (Cy3 labelled) was competitively hybridised against a common pooled-reference sample (Cy5 labelled), which comprised equal amounts of aRNA from each of the samples used in the study. This design permits valid statistical comparisons across all treatments to be made. The entire experiment comprised 24 hybridisations - 2 lipid phenotypes (Lean/Fat) × 2 diets (FO/VO) × 6 biological replicates.
2011-01-04 | E-TABM-1089 | biostudies-arrayexpress