Bulk RNA-sequencing data of mouse suprachiasmatic nucleus and habenula at 4 different timepoints throughout the day in resilient, susceptible and stress-naive phenotypes following chronic social defeat stress. All the data, as well as the the description of the dataset, are available in the 'narain_et_al-2024-translational_psychiatry'. The relevant description is to be found in the 'README_narain_et_al-2024-translational_psychiatry.md'.