In 2006 the ciliated protozoan Tetrahymena thermophila genome was sequenced and predicted gene annotation has been completed. Tetrahymena is a unicellular model organism that has been used for molecular and cellular biological discoveries such as telomeres, histone modifications, and catalytic RNA. Now experimental research must be done to further functionally annotate the Tetrahymena genome, which will increase the usefulness of this model organism for many areas of study. In order to further annotate the genome of Tetrahymena and start functional and proteomic annotation of this organism we have taken on a multi-course inquiry-based approach to class laboratories in cell and molecular biology curriculum at Missouri State University. In this approach the predicted Tetrahymena genes are cloned into entry plasmids in an introductory level biomedical science lab (performed by Missouri Sate University honors students). The cloned genes can then be used in upper division molecular biology classroom labs in order to characterize the expression, localization, and protein interactions. Students in all classes conduct bioinformatics and gene expression experiments in order to further characterize and confirm the annotation of the predicted genes. Through this multi-classroom inquiry-based laboratory approach students learn the basic techniques required for laboratory research in science as well as aid in the further genomic and proteomic annotation of the Tetrahymena thermophila genome. The students classroom laboratory experience culminates in the submission of their results for publication on the Student/UnPublished Results database (SUPRdb) website (http://ciliate.org/suprdb/; for student classroom research data). This allows any scientific researcher in the field to see what genes have been studied and the most current results and resources for each gene.