In this study, we measured the relative transcript expression of 45 target genes and 3 normalizer genes in liver samples of 120 Atlantic salmon that were subjected to 3 different climate scenarios in a tank-based system.Atlantic salmon were exposed to following treatments: (1) Control (CT) constant temperature of 12°C and 100 % air saturation; (2) Warm&Normoxic (WN) incremental temperature increase (1°C per week from 12 - 20°C) at 100% air saturation; and (3) Warm&Hypoxic (WH) decrease in oxygen content of 70% air saturation over one week, followed by two weeks of acclimation to this oxygen level, and then incremental temperature increase (1°C per week from 12 - 20°C) at 70% air saturation. Liver samples were taken from 8 fish per treatment group (CT, WN and WH) at 5 different temperature measuring points: 12°C, 16°C, 18°C, 19°C, and 20°C. For each treatment group, we used 8 biological fish replicates (4 fish from 2 tank replicates). The sampling during the simulated seasonal temperature increase was performed 3 days after reaching the temperature level of interest (12°C-initial, 16°C-3days, 18°C-3days, 19°C-3days, 20°C-3days). Once the maximum temperature increase of 20°C was reached, an additional sampling after 4 weeks at 20°C was carried out (20°C-4weeks). After each temperature challenge eight fish per per tank replicate (n = 8, N = 24) were euthanized with 400 mg L^-1 of tricaine-methane-sulfonate. Liver tissues (100 mg per sample) were rapidly dissected from fish, placed in RNase-free 1.5 mL tubes, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extractions were performed.The relative transcript expression values of 45 genes of interest (GOIs) and 3 normalizers were assessed for 8 individual fish samples per 3 treatment groups at 5 sampling time points (n = 8, N = 120). Real-time qPCR Fluidigm Biomark HD system based on 96.96 dynamic arrays (GE-arrays) was employed according to the manufacturer's instructions (Fluidigm, Biomark HD). The transcript levels of 48 genes were measured in two technical replicates, while we included two no template controls (NTCs), two controls for genomic DNA contamination (no-reverse transcription 'no-RT') and two linker samples for inter-run and between-run calibration.In this data submission file, we provide the 'mean threshold cycle (CT) values' for 45 GOIs and 3 normalizer genes that were calculated from two technical replicates and were measured with GE-fast 96.96 PCR protocol and Fluidigm Biomark HD system.This experiment was performed as part of the project 'Mitigating the Impacts of Climate-Related Challenges on Salmon Aquaculture (MICCSA)' within the years 2017-2020.