Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Atlantic salmon (Salmo salar) liver sampled at various stages through smoltification

ABSTRACT: The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate a transcriptome data from livers throughout smoltification and after seawater transfer. In this experiment two groups of Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the experiment group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. The second control group received constant light throughout the experiment. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Salmo salar

SUBMITTER: Simen Sandve

PROVIDER: E-MTAB-11746 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATAC-seq of Atlantic salmon (Salmo salar) liver sampled at various stages through smoltification

Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate ATAC-seq data from livers throughout smoltification and after seawater transfer to assess the differences in chromatin accessibility. In this experiment Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.

2024-02-02 | E-MTAB-13743 | biostudies-arrayexpress

Impact of short photoperiod length on smoltification (RNAseq)

Project description:This experiment was set up to evaluate the effect of the duration of a short photoperiod (winter-like conditions, 8 hours light, 14 hours dark) on the smolt transcriptome in liver and gill. Fish were kept at constant light before fish were split between treatment tank or control tanks. Treatment tanks either experienced 2 weeks of short photoperiod or 8 weeks of short photoperiod. The control fish were kept in constant winter-like conditions. After winter, the fish were brought back to constant light for 4 weeks. Sampling was done before transition to short photoperiod, at the end of winter period and four weeks after transition back to constant light. Control fish were sampled at the same time points as the treatment group.

2022-05-20 | E-MTAB-10526 | biostudies-arrayexpress

Hepatic gene expression in chinook salmon (Oncorhynchus tshawytscha) exposed to sewage

Project description:Hepatic transcriptional profiling of fish exposed to sewage to evaluate temporal and concentration trends. Two experiments (Year 1 and 2), each with 6 concentrations (0%, 0.05%, 0.1%, 0.7%, 2% and 5/10%) of sewage diluted in seawater at 4 timepoints (1, 4, 8 and 16 days).

2012-12-01 | E-GEOD-38925 | biostudies-arrayexpress

RNAseq of farmed and wild Atlantic salmon fed vegetable oil or fish oil or phospholipid diet from first feeding

Project description:Farmed and wild Atlantic salmon was given either vegetable oil (low DHA and EPA) feed or fish oil (high in DHA and EPA) feed or phospholipid (high in phospholipid) feed from start of feeding. We sampled and RNAseq two tissues (pyloric caeca and liver) on day 0, day 48, day 65 and day 94 after initial feeding.

2019-10-30 | E-MTAB-8306 | biostudies-arrayexpress

Analysis of the Gulf toadfish intestinal proteome response to chronic hypersalinity exposure

Project description:The marine teleost intestine plays a vital role in whole body salt and water homeostasis. Marine fish must drink seawater in order to rehydrate, and processing of that seawater throughout the gastrointestinal tract allows for the extraction of water from this highly hyperosmotic source. Although the molecular mechanisms of this process have been the subject of much investigation, numerous questions remain. Here, Gulf toadfish (Opsanus beta) were acclimated to normal seawater (35 ppt) of hypersaline seawater (60 ppt) and changes in the anterior intestine, posterior intestine, and intestinal fluid proteomes were investigated using a shotgun proteomics approach employing isobaric TMT tags.

2018-06-26 | PXD005923 | Pride

Photoperiodic control of smoltification

Project description:This experiment is intended to provide information about transcriptional changes in the gill of Atlantic salmon during smoltification, in comparison with juvenile salmon not given the appropriate photoperiodic stimuli. Also, transcriptional changes due to osmotic stress (24H salt water challenged) will be recorded. This to better understand the transformation of the gill from a fresh water-type to a salt water-type, and possibly identify novel and important genes that are dependent upon a specific photoperiodic history for their expression. Additionally the data can be used to observe the shift in salt water response as the juvenile salmon goes through smoltification. Experimental workflow: All fish started on 24H light (LL), after one week, half of the fish were moved to short photoperiod (8:16, SP). The rest remained on LL throughout. After eight weeks, half of the fish on short photoperiod were moved back onto 24H light (SPLL). Remaining fish continued under 8:16. After another eight weeks the experiment was ended. Fish were sampled on days 0, 32, 53, 68, 89 and 110. On each sampling occasion fish were sampled directly from fresh water (FW), and from a 24H salt water (SW) stay, transferred the previous day. Weight and length was noted. Gill tissue was the taken and placed in RNAlater. Additionally plasma for measuring hypoosmoregulatory capacity was taken.

2019-09-12 | E-MTAB-8276 | biostudies-arrayexpress

Transcriptome effects of persistent organic pollutants in the liver of Atlantic cod (Gadus morhua)

Project description:In the North Sea and adjacent North Atlantic coastal areas fish experience relatively high levels of persistent organic pollutants. The aim of this study is to compare the mode of actions of environmentally relevant concentrations of halogenated compounds and their mixtures in Atlantic cod. Juvenile male cod were fed mixtures of chlorinated (PCBs, DDT analogs, chlordane, lindane and toxaphene), brominated (PBDEs) and fluorinated (Perfluorooctanesulfonate/PFOS) compounds for one month. One group received a mixture of all three compounds. Transcriptome analysis of liver samples was performed to identify the main affected pathways. Accumulated levels of chemicals in cod liver reflected concentrations found in wild fish. Pathway analysis revealed that the treatment effects by each of the three groups of chemicals (chlorinated, brominated and fluorinated) converged on activation of the unfolded protein response (UPR). The results of our transcriptomics analysis suggest that the UPR pathway is a sensitive common target of halogenated organic environmental pollutants

2023-01-04 | E-MTAB-12338 | biostudies-arrayexpress

HEPATIC GENE EXPRESSION PATTERNS IN JUVENILE TURBOTS (Scophthalmus maximus) AFTER EXPOSURE TO STYRENE (PRAGMA, a pragmatic and integrated approach for the evaluation of environmental impact of oil and chemical spills at sea)

Project description:Accidental spills of chemical or oil tankers such as Levoli Sun or Prestige have recently impacted the European seas. The analysis of the genes regulated by exposure to spilled chemical substances could help elucidating adaptatory and compensatory pathways that may participate in pathogenesis in marine biota. Hepatic expression profiles of male juvenile S. maximus exposed to a nÂº2 fuel-oil (FO) and to styrene were studied employing a turbot custom microarray containing 2715 3â-UTR biassed single-sequences, many of them unannotated. Hybridisations identified 169 and 293 genes significantly regulated after 3 and 14 days of exposure to FO, respectively. Typical PAH responsive genes such as AhRR, ARNT2, CYP1A1 and GST were significantly upregulated. Exposure significantly affected genes involved in protein metabolism, synthesis being the most regulated pathway with ribosomal proteins and various translation factors overexpressed. Protein synthesis could participate in compensatory pathways after FO induced protein damage. Additionally, two weeks of exposure resulted in the upregulation of ras pathway genes. Regarding styrene, gene expression was very variable within experimental groups and only 2 genes were significantly regulated after 3 days of exposure. After 1 week of exposure styrene modified the expression levels of 44 genes. Most highly regulated genes, that may constitute new biomarkers of exposure to styrene, included those coding for estrogen-responsive finger protein, transmembrane 9 superfamily member 4 or selenoprotein-T, but the only pathway found to be significantly regulated was once again that of protein synthesis. Funded EU project PRAGMA, Spanish MEC (CANCERMAR), Basque Government (Consolidated Research Groups GIC07/26-IT-393-07). Turbots were exposed to styrene and to seawater control. After 3 and 7 days of exposure turbots were in situ dissected and liver was extracted, inmersed in RNAlater and frozen in liquid N2

2016-07-31 | E-GEOD-43359 | biostudies-arrayexpress

Transcriptome analysis of capelin (Mallotus villosus) liver slice culture exposed to benzo[a]pyrene

Project description:Capelin (Mallotus villosus) is one of the important fish species in the arctic marine foodweb that could be vulnerable to contaminant exposure from offshore petroleum related activities. The study was conducted to map transcriptome responses in capelin liver slice culture exposed to benzo[a]pyrene (BaP). BaP is a polyaromatic hydrocarbon (PAH) which is among the most toxic compounds found in crude oil. Ex vivo liver slices culture was performed under 10 µM BaP exposure for 72 h and transcriptome analysis (RNA-seq) analysis was performed to characterize de novo transcriptome of the liver and identify genes responding to BaP exposure.

2024-09-08 | E-MTAB-13934 | biostudies-arrayexpress

RNAseq of Atlantic salmon with CRISPR/Cas9-mediated mutation of delta-5 and multiple delta-6 fatty acyl desaturase genes

Project description:The present study used CRISPR/Cas9 technology to generate two knockout strains of salmon by mutating 1) all fads genes simultaneously (delta-5fad, delta-6fad-a, delta-6fad-b and delta-6fad-c), and 2) delta-6fad-b and delta-6fad-c genes. Liver was taken and RNA-seq was used.

2020-05-31 | E-MTAB-8319 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data