{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Elzbieta Krol"],"organism":["Salmo salar"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17447"],"description":["We used gill RNA-seq and histopathology to compare commercially farmed autumn and spring smolts at two sampling times approximately 8 months apart, testing whether transcriptomic and histopathological profiles were more strongly associated with smolt production strategy or time in seawater."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Fish rearing and seawater transfer Juvenile Atlantic salmon (Salmo salar) of the Fanad commercial strain were reared at Scottish Sea Farms (SSF) Knock Hatchery under continuous light conditions (LL, 24 h light/0 h dark) from the point of ova input on 18 January 2017. In September 2017, approximately half of the cohort was transferred to a freshwater farm at Loch Frisa for on-growing and smoltification manipulation. These fish were exposed to the naturally shortening photoperiod of early autumn (September–October), followed by a 4-week period of LL in November 2017. This light regime was designed to mimic natural photoperiodic cues that trigger parr–smolt transformation, enabling the production of autumn (A) smolts (i.e., smolts that enter seawater in autumn, under one y","Nucleic Acid Extraction - RNA extraction  Total RNA extractions were performed on the entire selected gill arches (24 smaller fish at sampling time 1) or on three individual transverse sections taken from the same selected gill arch for each fish (24 larger fish at sampling time 2). In both cases, arch tissue was removed to leave only full-length filaments for processing. Total RNA was isolated by homogenising ~100 mg of gill tissue in TRIzol® Reagent (Ambion by Life Technologies, Carlsbad, CA, USA), using 3 mm tungsten carbide beads and a TissueLyser II Disruption System (Qiagen GmbH, Hilden, Germany). RNA concentrations were quantified by spectrophotometry (NanoDrop Technologies, Wilmington, DE, USA), and RNA integrity was assessed by electrophoresis (Agilent Technologies, Santa Clara, C","Library Construction - Library preparation  Library preparation and sequencing were performed by Edinburgh Genomics at the University of Edinburgh (UK). The libraries for all 48 gill RNA samples were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA), following the manufacturer’s instructions.","Sequencing - RNA sequencing  Paired-end sequencing (50 bp from each end) was conducted on the NovaSeq 6000 system with S1 flow cell (Illumina, San Diego, CA, USA) at a sequencing depth of ~36.5 million read pairs per library. The raw reads in CBCL format were converted to FastQ format with bcl2fastq2 Conversion Software v2.19.1 (Illumina, San Diego, CA, USA)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Read mapping and gene-level quantification  The quality of the sequencing data was assessed with FastQC v0.11.8 (Andrews, 2010). Sequencing adapters were removed using Flexbar v3.4.0 (Dodt et al., 2012). Filtered reads were then mapped to the Atlantic salmon genome assembly Ssal_v3.1 (GCA_905237065.2) using HISAT2 v2.1.0 (Kim et al., 2015) with the stranded parameters. Aligned reads were counted at gene locations using featureCounts v2.0.1 (Liao et al., 2014). For multi-mapping reads, a fractional count (1/n) was assigned to each reported alignment, where n reflects the total number of alignments reported for that read.","Data Transformation - RNA-seq read quality was assessed using FastQC v0.11.8. Sequencing adapters were removed using Flexbar v3.4.0. Filtered paired-end reads from each sample were mapped to the Atlantic salmon genome assembly Ssal_v3.1 (GCA_905237065.2) using HISAT2 v2.1.0 with stranded parameters. Aligned reads were counted at gene locations using featureCounts v2.0.1. Multi-mapping reads were assigned fractional counts, with a count of 1/n assigned to each reported alignment, where n is the total number of alignments reported for that read. Lowly expressed genes were filtered by retaining genes with at least 1 count per million (CPM) in at least 10 of the 48 samples, resulting in 30,749 genes. The submitted processed data file contains filtered raw gene-level counts. For downstream anal"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Salmo salar"],"pubmed_authors":["Elzbieta Krol"],"additional_accession":[]},"is_claimable":false,"name":"Gill transcriptomics of Atlantic salmon smolts","description":"We used gill RNA-seq and histopathology to compare commercially farmed autumn and spring smolts at two sampling times approximately 8 months apart, testing whether transcriptomic and histopathological profiles were more strongly associated with smolt production strategy or time in seawater.","dates":{"release":"2026-08-10T00:00:00Z","modification":"2026-08-10T01:00:38.902Z","creation":"2026-07-29T11:30:04.121Z"},"accession":"E-MTAB-17447","cross_references":{"ENA":["ERP202999"],"Biostudies":["E-MTAB-8855"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}