biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsPatricia Rivera Mayotranscription profiling by arraySalmo salarSalmo salarhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15367This experiment aimed to compare the global gene expression profiles between precociously maturing and immature male Atlantic salmon (Salmo salar) of the Lochy strain reared in freshwater. Transcriptome analyses were conducted in brain, gonad, and liver tissues using one-color microarrays to identify differentially expressed genes (DEGs) and reveal enriched functional pathways associated with sexual maturation.biostudies-arrayexpressLabeling - The labeling protocol was performed by ThermoFisher according to the GeneChip™ WT PLUS Reagent Kit USER GUIDE / Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays, specifically mentioned in the section “Fragment and label single-stranded cDNA”, which specifies: “the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of single-stranded cDNA is required for fragmentation and labeling.”Hybridization - The hybridization to array protocol was performed by ThermoFisher according to the GeneChip™ WT PLUS Reagent Kit USER GUIDE / Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays, specifically mentioned in the section “Array plate hybridization on the GeneTitan™ MC Instrument - Target hybridization setup for array plates / Hybridization setup”, which involves the steps of preparing solutions by regulating temperatures , vortexing and/or centrifugating them if necessary, preparing the Hybridization Master Mix and the Hybridization Cocktail, and a final hybridization setup on the GeneTitan™ MC Instrument.Nucleic Acid Extraction - Tissue samples were processed using the standard TRIzol® (Invitrogen) protocol following the manufacturer's guidelines, briefly consisting of a homogenization phase submerging sample in TRIzol®, beads and using an MP FastPrep-24® homogenizer, followed by a separation phase using chloroform, an RNA precipitation phase with isopropanol, an RNA washing phase with 75% ethanol, to finally resuspend RNA in nuclease free water, slightly modifying incubation times and/or temperatures as best suited our process, and including an additional acetate precipitation phase only when required, to achieve sample purity. For all samples, RNA quantification was performed using an NP80-Touch nanophotometer, and RNA integrity was assessed by electrophoresis in a SYBR Safe (Thermo Fisher)-stained 2% agarose-gel, prepared with 1X TAE buffer and DEPC-treated distilled water.Sample Collection - Prior to sampling, sterilized dissection kits—including forceps, scalpels, and scissors—were prepared. Cryovials (2 mL screw-cap tubes) were pre-filled and labeled, each containing 1 mL of RNAlater® Tissue Collection reagent (Thermo Fisher). At the freshwater fish farm, the workspace was prepared by disinfecting surfaces with 70% alcohol, arranging Kraft paper all over the working surface and setting up all the necessary materials and equipment for data and sample collection. During each sampling times, once euthanized with an overdose of commercial benzocaine, each fish was assessed to record its morphometric variables, which included full body weight and length, and gonad weight to calculate gonadosomatic index (GSI), fish were then dissected, and brain, liver, and gonad tissue samples were collected and preserved in RNAlater. Once collected, all samples were immediately stored at 4°C for around 8 hours, to later be transported to the laboratory facilities while stored at approximately 10°C for around 12 hours, and finally, at the laboratory, samples were stored at -80°C until RNA extraction.Scaning - The scanning and feature extraction protocol was performed by ThermoFisher according to the GeneChip™ WT PLUS Reagent Kit USER GUIDE / Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays, specifically mentioned in the section “Array plate hybridization on the GeneTitan™ MC Instrument - Process WT array plates on the GeneTitan™ MC Instrument”, where the steps for this process are detailed and include using the GeneTitan™ ZeroStat AntiStatic Gun on the wells of the stain tray labeled “GeneTitan™ Stain Tray P/N 501025”, aliquoting 105 µL of Stain Cocktail 1 & 3 into the GeneTitan™ stain tray, using the antistatic gun on the stain tray cover, placing the cover on top of stain tray 1 after removing the static electricity, using the fourth scan tray cover provided with the GeneTitan™ Consumables Kit to cover the scan tray, and loading all the consumables including the HT array plate into the GeneTitan™ MC Instrument according to instructions provided in the GeneTitan™ Instrument User Guide for Expression Array Plates.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsPatricia Rivera MayoData Transformation - \"Native\" processed files (.CHP) were generated by sst-rma normalization and summarization from Affymetrix “.CEL” files, using Transcriptome Analysis Console (TAC) software. This option summarizes the probes into a single signal for each probeset, and converts “.CEL” files to “.CHP” files without performing a differential expression analysis.falseMaturation in males of Salmo salarThis experiment aimed to compare the global gene expression profiles between precociously maturing and immature male Atlantic salmon (Salmo salar) of the Lochy strain reared in freshwater. Transcriptome analyses were conducted in brain, gonad, and liver tissues using one-color microarrays to identify differentially expressed genes (DEGs) and reveal enriched functional pathways associated with sexual maturation.2026-02-10T00:00:00Z2026-02-10T02:02:01.977Z2025-07-18T13:08:56.325ZE-MTAB-15367EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815