RNA-Sequencing of HEK293 During Adeno-Associated Virus Production [EXPA]

Recombinant viral vectors such as adeno-associated viruses (AAV) have emerged as a key tool in gene therapy applications. Despite extensive research efforts aimed at increasing production yields, the intricate molecular mechanisms that govern the synthesis of viral vectors within host cells remain largely unknown. The interplay between viral replication and cellular biosynthetic processes is complex and not fully understood, which poses challenges for effective manipulation. This study uses transcriptomics and RNA sequencing to investigate the cellular processes underlying viral vector production. Transcriptomics examines RNA molecules and their role in gene expression and has become invaluable in modern biological research. The advent of cost-effective, high-throughput sequencing technologies enables the comprehensive analysis of transcriptomes, providing valuable insights into gene regulation and cell signalling pathways. This study takes a strategic approach to deciphering the cellular mechanisms involved in viral vector production by utilising RNA-Seq data from a commercially available HEK293 suspension cell line. This study emphasises the importance of data-driven methodologies in advancing cell line development and optimising viral vector production. The RNA-Seq dataset comprises samples collected from a commercially available HEK293 suspension cell line. The experimental design involved transfecting these cell lines with a two-plasmid system and a polymer-based transfection reagent to facilitate AAV synthesis. Samples were harvested 18 hours after transfection to capture the gene expression profiles in these conditions. For reference purposes, untransfected cultures were also sampled at the same time. These cultures received PBS instead of plasmid DNA and the transfection reagent.