Legend for the file deposited on Dryad
Table S1: Sample, RNA quality, gene counts, and library information. Sheet “Samples All ” lists all samples collected (sample ID and Admera Health ID for QuantSeq and for NEB) with information about the treatment group they belong to, tissue type, sampling method, length and weight of the fish, RIN value, and RNA concentration. Sample size used for each comparison and divided for tissue type, treatment group, and library preparation is also indicated. Sheet “QuantSeq ” lists all samples used for the QuantSeq library with the following information for each sample: treatment group, sample ID, Admera Health ID’s, tissue type, sampling method, RIN value, concentration, raw read count, read count after mapping the randomly selected 11 million reads, and percentage of uniquely mapped genes on the reference genome. Sheet “NEB ” lists all samples used in the NEB library detailing for each sample the following: treatment group, sample ID, Admera Health ID’s (and new Admera Health ID if existing), tissue type, sampling method, RIN value, concentration, raw read count (PE and single), read count after mapping the randomly selected 40 million reads, and percentage of uniquely mapped genes on the reference genome.
Table S2: Output results of the Differential Expression Analysis . Results of Differential Expression Analysis done with DESeq2 for all comparisons, each of them presented on a separate sheet. Groups 1, 2, and 3 refer to sampling by netting, electrofishing, and electrofishing with processing 5 min after euthanasia, respectively.
Table S3: Summary of gene expression patterns for different sampling methods and tissue types. The total numbers of genes with detectable expression for each sampling/tissue comparison are indicated along with the number and proportion of genes with significantly higher gene expression in one of the two tissues being compared for each sampling method.
Table S4: Summary of gene expression patterns for different sampling methods and tissue types. The total numbers of genes with detectable expression for each sampling/tissue comparison are indicated along with the number and proportion of genes with significantly higher gene expression in one of the two tissues being compared for each sampling method.