{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE319nnn/GSE319528/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Escherichia coli BW25113"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE319528"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"A Course-Based Undergraduate Research Experience (CURE) Using Transposon-directed insertion sequencing (TraDIS) to Identify Genes Required for Bacteriophage P1 Propagation in Escherichia coli","description":"Understanding gene function through forward genetic screens remains foundational to microbial genetics. Here, we describe the design and implementation of a multi-week course-based undergraduate research experience (CURE) embedded within a third-year Microbial Genetics course. In this CURE, students construct a high-density Tn5 transposon insertion library in Escherichia coli, challenge the library with bacteriophage P1, and use Transposon-Directed Insertion-site Sequencing (TraDIS) coupled with statistical analysis (edgeR) to identify genes required for phage propagation. Students perform transposome electroporation, phage infection assays, genomic DNA extraction, high-throughput sequencing data processing in Galaxy, differential insertion analysis, visualization in Artemis, and Gene Ontology enrichment analysis. The project integrates wet-lab microbiology, molecular genetics, and bioinformatics while modeling an authentic forward genetic screen. This CURE emphasizes experimental design, genome-wide functional analysis, statistical reasoning, and interpretation of large-scale sequencing data. The curriculum is adaptable to other bacterial species, phage systems, or selective pressures and provides a scalable framework for integrating authentic genomics research into upper-level microbiology courses.","dates":{"publication":"2026/09/09"},"accession":"GSE319528","cross_references":{"GSM":["GSM9519242","GSM9519245","GSM9519243","GSM9519244"],"GPL":["18995"],"GSE":["319528"],"taxon":["Escherichia coli BW25113"]}}