Supplemental materials for "Diploid and triploid chinook salmon (<em>Oncorhynchus tshawytscha</em>) have altered microRNA responses in immune tissues after infection with <em>Vibrio</em> <em>anguillarum</em> "

Supplemental files for study investigating the impact of <em>Vibrio</em> <em>anguillarum</em> infection on diploid and triploid Chinook salmon (<em>Oncorhynchus tshawytscha</em>) was investigated to identify if there was any significant immune regulation by microRNAs (miRNA). Small RNAs from hindgut (hg), head kidney (hk), and spleen (sp) were sequenced to determine if miRNA transcript abundance was altered due to ploidy and infection in nine-month old full-sibling diploids and triploids. MiARma-seq and bowtie1 were utilized to align reads to the Chinook salmon genome, and then read abundance associated with miRNA genes quantified using FeatureCounts. Read counts were then analyzed using DESeq2 to identify differentially expressed miRNA between ploidies as well as after infection in all three tissues. Finally, targets of differentially expressed miRNA were predicted using miRanda and pathway impacts predicted using KEGG analysis. <br> Files included: <strong>run_log.log</strong> - miARma-seq logfiles for hindgut (hg), head kidney (hk), and spleen (sp) <strong>stats.log</strong> - miARma-seq stats information for hindgut (hg), head kidney (hk), and spleen (sp) <strong>miarma.cadonic.known.tshawyt.sample.ini</strong> - initiation file for miARma-seq which includes all parameters that were utilized to analyze raw reads <strong>deseq2_cadonic_sample.R</strong> - sample of R code for DEseq2 used to identify differentially expressed miRNA genes <strong>Sasa_Ensembl_3UTR_clean.fasta </strong>- File of 3' untranslated region (UTR) for annotated genes in Ensembl biomart (Ensembl release 105) that was analyzed with miRanda (version v3.3a) to predict miRNA-mRNA relationships. Sequences with unavailable UTRs were cleaned by replacing empty spaces with N using "sed -e '/^[^&gt;]/s/[^ATGC]/N/g' Sasa_Ensembl_3UTR.txt &gt; Sasa_Ensembl_3UTR_clean.fasta". <strong>cadonic_2023_Bioinformatics_protocol_extended.docx - </strong>Extended explanation for the bioinformatic steps and justification for the workflow used in the study.