Cotton leaf curl disease (CLCuD) is a devastating viral disease for the crop in Asia. Despite extensive research, the development of utterly resistant cotton varieties remains elusive, mainly due to a limited understanding of the molecular dynamics between host and virus. Hence, to understand the molecular mechanisms affected by CLCuD infection, this study involves transcriptomics analysis of Gossypium hirsutum genotypes, specifically HS-6 (CLCuD-susceptible). Plants were divided into two groups - infected plants and control plants; infected plants were inoculated with Cotton leaf curl virus through infected whiteflies, and control plants were raised in a whitefly-free environment. Leaves from the infected plant and control plants were collected separately and subjected to next-generation paired-end sequencing using Illumina Novaseq 6000.