biostudies-arrayexpressMarianne IversenSalmo salarhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16457RNA-seq dataset used to compare the transcriptome of the Atlantic salmon (Salmo salar) tongue and olfactory rosette, in control and infected fish (Yersinia ruckeri). Tongue samples from control also used to describe gene expression in the salmon tongue.biostudies-arrayexpressLibrary Construction - Total RNA samples were sent to the Norwegian Sequencing Centre (OUS, Norway). A strand-specific TruSeq RNA Library Prep Kit (Illumina, CA, USA) was used to prepare RNA-seq libraries using the manufacturer’s protocol.Sequencing - The libraries were pooled and sequenced on one lane of NovaSeq X (Illumina, CA, USA) S4 flowcell, 150 bp paired-end reads.Sample Collection - Tongue samples for basal transcriptome profiling (RNA-seq) were collected from brackish water-adapted Atlantic salmon (~120 g, n=5) reared in a recirculating aquaculture system at 12 ppt salinity and 12°C. Fish were fasted for 24 hours before sample collection and euthanised using an overdose of Benzoak vet (ACD Pharmaceuticals AS, Norway). Tongue samples were preserved in RNAlater™ Stabilization Solution (Thermo Fisher Scientific, Lithuania), kept overnight at 4oC, and then transferred to -20oC until RNA isolation.Nucleic Acid Extraction - RNA of all samples was isolated using the Agencourt RNAdvance™ Tissue Total RNA Purification Kit (Beckman Coulter Inc., USA) using the Biomek 4000 automated workbench station (Beckman Coulter, Inc.). To provide an en masse representative of the organ, the entire tongue was homogenised first using ceramic beads in FastPrep-96™ (MP Biomedicals LLC, USA) for 2 mins before a small portion of the homogenate (ca 10 mg) was used for RNA isolation. RNA concentration and purity were assessed using a NanoDrop 8000 Spectrophotometer (Thermo Fisher Scientific). Samples designated for RNA sequencing underwent additional quality control using an Agilent 2100 Bioanalyzer (Agilent, California, USA). The RNA integrity number (RIN) values of all samples were above 8.0.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Scaling factors for conversion to normalised effective library sizes were calculated by applying the TMM method. Normalised effective library sizes were used to calculate counts-per-million (cpm), which will be referred to as the normalised counts.Sequence Alignment - Raw sequence data were pre-processed using BBDuk (part of BBMap v.38.18, ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149) to remove/trim adapter sequences and low-quality reads. HISAT2 (v.2.2.1, (parameters: –rna-strandness RF) was used when aligning the data to the Salmo salar Ssal V3.1 reference genome (ref/source). Rsubread (v.1.5.0-p1) was used to estimate the number of reads aligning to the reference genome Ssal V3.1.110 GTF annotation.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNASalmo salarCarlo LazadoMarianne IversenfalseRNA-seq of Atlantic salmon tongue and olfactory rosette -including infection trialRNA-seq dataset used to compare the transcriptome of the Atlantic salmon (Salmo salar) tongue and olfactory rosette, in control and infected fish (Yersinia ruckeri). Tongue samples from control also used to describe gene expression in the salmon tongue.2026-01-31T00:00:00Z2026-05-27T16:38:23.278Z2025-12-22T10:28:56.41ZE-MTAB-16457ERP186896EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184