Additional file 5 of A comprehensive analysis of Atlantic salmon gonad and pituitary transcriptomes identifies novel players in sexual maturation

Additional file 5. ms_salmon_gnpt_rnaseq_supplementary_tables. Table S1. Overview of 98 sequenced Atlantic salmon tissue samples with associated sample metadata, RNA extraction and quality assessment (QA) data Each row corresponds to one RNA sample. Columns include sample ID, fish ID, tissue type, sex, maturation stage, RNA concentration (ng/μL), RNA integrity number (RIN), 5S-rRNA ratio, and corrected RNA concentration based on 5S-rRNA contamination (Correct_Conc = Conc × (1 - 5S-rRNA ratio)). Tablae S2. Overview of quality assessment (QA) of RNA-sequencing raw data across four Atlantic salmon tissues. This table summarizes the sequencing quality metrics per tissue. Columns include the total number of raw reads (in millions), number of reads that passed quality filtering, number of low-quality reads removed, the percentage of reads passing filter (Passed filter ratio), and the estimated duplication rate. Table S3. Intergenic transcript representation across Atlantic salmon tissues. This table lists intergenic transcript IDs, the total number of samples in which each transcript is detected, and the number of samples where it appears in each tissue (Immature testis, Mature testis, Ovary, Pituitary). Percent columns show the proportion of samples expressing the transcript within each tissue type. Table S4. Benchmarking of two public Atlantic salmon testis RNA-seq datasets using our transcriptome analysis pipeline. This table shows alignment statistics for RNA-seq samples from two publicly available datasets (PRJNA380580 and PRJNA550414). For each sample, the table reports the total number of input reads, the number and percentage of uniquely mapped reads, and the number and percentage of multi-mapping reads, based on alignment against our transcriptome annotation. Table S5. Transcript class codes assigned by gffcompare for benchmark RNA-seq sample assemblies versus the Atlantic salmon reference annotation. This table shows the number and percentage of transcripts assigned to each class code for RNA-seq samples from two public datasets (PRJNA380580 and PRJNA550414). The transcripts were obtained by assembly and compared to the reference annotation using gffcompare. Table S6. Transcript class codes assigned by gffcompare for benchmark intergenic transcripts in RNA-seq sample versus the intergenic transcripts in unified transcriptome annotation from this study. This table shows the number and percentage of intergenic transcripts assigned to each class code for RNA-seq samples from two public datasets (PRJNA380580 and PRJNA550414) comparing to the intergenic transcripts identifed in unified transcriptome annotation using gffcompare. Table S7. Modules identifed using WGCNA and the enricched GO term in each module. This table contains full tables with all the significant GO terms enriched (p.adjust < 0.05). Table S8. Expression and enrichment information of newly characterized protein-coding genes identifed enriched in GO term. This table shows 69 newly characterized protein-coding genes enriched GO terms, and its expression information indluding upregulated status, tau values, WGCNA module, Table S9. Candidate lncRNA-protein coding gene pair across five major tissue-related module. This table contains the information of the 104 lncRNA-protein coding gene pairs, including expression (tua value, preferred expressed tissue, upregulated in single tissue) in both lncRNA and its partner protein-coding gene. And orientation of the interactions and localisation of the interactions between lncRNA and its partner gene.