biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsLars GrønvoldIllumina NovaSeq 6000RNA-seq of coding RNAEsox luciusEsox luciushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17634The REWIRED study investigates the evolution of gene expression after the salmonid-specific whole-genome duplication. Strand-specific mRNA sequencing was performed across six salmonid (Hucho hucho, Thymallus thymallus, Oncorhynchus kisutch, Oncorhynchus mykiss, Salvelinus alpinus and Salmo salar) and six non-salmonid teleost fish species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Novumbra hubbsi, Esox lucius and Umbra pygmaea), comparing brain, liver, gill and spleen from male and female fish. Additional tissues comprise muscle from Esox lucius and Salmo salar, and heart, skin and male gonad from Salmo salar. The dataset contains 205 sample records, represented by 287 paired-end sequencing runs (574 FASTQ files). Libraries were prepared using the Illumina TruSeq Stranded mRNA biostudies-arrayexpressSample Collection - Fish were anesthetized with tricaine. Liver was removed from the fish and perfused by injection with fresh wash buffer (1x HBSS -Mg,-Ca, 1 mM EDTA, 10 mM HEPES, pH7.4) prior to freezing on dry ice. All other tissue samples were immediately frozen on dry ice. Samples were stored at -80°C until RNA extraction.Sequencing - Sequencing was performed by Novogene with a paired-end 150-base design. The standard-depth dataset had a target of 25 million read pairs per sample, and selected Esox lucius and Salmo salar samples had a target of 100 million read pairs for alternative-splicing analysis. Batch2 contains additional sequencing of libraries with insufficient initial depth. Each paired FASTQ dataset is retained as a separate run linked to its sample, including repeat sequencing at different depth targets.Nucleic Acid Extraction - Total RNA was extracted from tissue samples using the Qiagen RNeasy kit following the manufacturer's instructions.Library Construction - Strand-specific cDNA libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA Sample Prep HS kit according to the manufacturer's protocol.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSimen SandveLars GrønvoldfalseMulti-tissue RNA-seq from 6 salmonids and 6 non-salmonid teleost fishesThe REWIRED study investigates the evolution of gene expression after the salmonid-specific whole-genome duplication. Strand-specific mRNA sequencing was performed across six salmonid (Hucho hucho, Thymallus thymallus, Oncorhynchus kisutch, Oncorhynchus mykiss, Salvelinus alpinus and Salmo salar) and six non-salmonid teleost fish species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Novumbra hubbsi, Esox lucius and Umbra pygmaea), comparing brain, liver, gill and spleen from male and female fish. Additional tissues comprise muscle from Esox lucius and Salmo salar, and heart, skin and male gonad from Salmo salar. The dataset contains 205 sample records, represented by 287 paired-end sequencing runs (574 FASTQ files). Libraries were prepared using the Illumina TruSeq Stranded mRNA 2026-10-01T00:00:00Z2026-10-01T01:00:46.594Z2026-09-17T13:16:47.029ZE-MTAB-17634ERP206545EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184