Abstract
<jats:p>This dataset comprises downstream bioinformatic analysis results from RNA-seq experiments conducted on whitefish (Coregonus lavaretus) livers exposed to microcystin-LR (MC-LR). The study included MC-LR-treated and control (PBS) groups, with samples collected at 1, 6, and 9 days post-exposure. RNA was processed using the Illumina TruSeq Stranded mRNA protocol and sequenced (250–300 bp cDNA insert size, PE150, 50M reads, 15Gb). The bioinformatics workflow included quality control and trimming (FastQC, Trimmomatic), read alignment (STAR, Coregonus lavaretus AWG_v2 reference genome), transcript assembly (StringTie), transcript annotation (GffRead, BLAST), and open reading frame (ORF) prediction (TransDecoder). Differential expression analysis was conducted using DESeq2, with FPKM normalization performed by Ballgown. The dataset includes transcript sequences, gene annotations, raw count table, and GSEA-compatible files. Detailed methods and experimental design are described in the accompanying publication. Sample descriptions and raw sequencing data are available in the NCBI BioProject repository (PRJNA481245).</jats:p>