In vivo RNA sequencing was utilized to identify key molecular mechanisms responsible for Salmonella enterica serovar Typhimurium (STm) persistent infection. Our research team optimized an oral mouse infection model with STm to study both the acute and chronic infection mechanisms of this pathogen. We compared the transcriptomes of STm during acute and persistent infections within host tissue sites. Based on the results of these analyses, we conducted additional mouse experiments to gather more transcriptomic data to confirm our findings. Barbara Forró (current proxy) received the additional sequencing output (NGI Delivery: delivery06200, delivery06264) in early August 2022. After the data arrived, she extensively utilized the SNIC 2021/22-663 project and its extensions, SNIC 2022/22-849 and NAISS 2023/23-485 (small compute projects). Thanks to this transcriptomic data, we identified several target genes for further experiments, such as mouse infection studies using certain gene knockouts. We are anticipating new sequencing data this autumn (likely November 2024), which will require us to run the pipeline as Barbara did previously. The existing data has been migrated to Dardel at PDC while we await the new batch from our lab. Our current plan is to combine all our transcriptomic data, including those with low coverage, to extract biologically meaningful information from the zero-inflated dataset. Once we receive the complete dataset, we plan to test an autoencoder developed by Barbara, along with other state-of-the-art approaches, on a larger dataset. Therefore, I would like to request an extension of our access to the small computing project (SNIC 2022/22-849) and storage (SNIC 2022-23-446) now in Dardel. I would also like to request that in the extended project, Leyden Fernandez (leyden.fernandez@umu.se) be designated as the Principal Investigator (PI), with Barbara Forró remaining as the proxy.