Scripts and data for the manuscript "Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon"

This dataset supports the manuscript titled "Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon." It contains comprehensive RNA-seq count data from gill biopsies of approximately 3000 Atlantic salmon smolt, collected during the SynchroSmolt project. The data is supplemented with RNA-seq counts from two prior photoperiod smolt experiments (2013_shortdays and 2017_winterlength) and single-nucleus RNA-seq (snRNA-seq) data from an additional experiment.

Key Dataset Elements:- RNA-seq read counts and metadata for three experiments, detailing various growth, condition, and survival indicators.- Scripts for analysis include differential expression analysis, random forest model preparation and execution, and cell-type-specific gene analysis.- Intermediate data outputs such as normalized RNA-seq counts, results from differential expression analyses, and random forest model inputs and outputs.

This dataset facilitates the exploration of gene expression-based predictive modeling for seawater survival, revealing key insights into the influence of photoperiod history and developmental gene regulation on Atlantic salmon's transition to seawater.