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Title of the Project: RNA-Seq transcriptomic analysis in Arabidopsis thaliana Contact Name: Nadim Alkharouf Contact Address: Towson University, Towson, MD Contact Email: [email protected] Contact Phone: 410-704-3149 Background Information: The Alkharouf lab at TU seeks to identify genes and pathways in plants that are involved in resistance responses against pathogens using next generation sequencing (RNA-Seq). Project Goal: Plants are continually attacked by pests and pathogens. Billions of dollars are lost each year by farmers throughout the world due to plant diseases and pests. Arabidopsis thaliana is a model organism for plant biology. It has been widely used to study plant interactions against pathogen attack. Those studies have implicated a number of genes\pathways. Salicylic Acid (SA) production has been found to be the key defense compound produced by plants against a pathogen attack. This project is a joint research project with Dr. Hua Lu at the University of Maryland Baltimore County (UMBC). Dr. Lu is not only interested in plant defense but also with its relationship with the circadian rhythm of plants. The theory is that if a plant’s circadian rhythm is disrupted, then key defense pathways (like the production of SA) would also be affected. To that end she is studying Arabidopsis mutant plants that have a gene, called the lux gene, that has been silenced. The lux gene is known to be involved in circadian rhythm. We have RNA-Seq data from control plants and from the lux mutant plants. RNA was extracted at both 9 am and 9 pm for each. Your job is to analyze these RNA-Seq data, and compare them with each other to see if there are any key differences in defense related pathways. Specific Objectives: Objective 1: Align RNA-Seq reads to Arabidopsis thaliana genome. Objective 2: Conduct differential expression analysis by comparing mutant plants with control plants. Objective 3: Build a searchable database to allow scientists to mine the data for useful information Objective 4: Using GO ontologies and the KEGG pathway database, identify key genes and pathways that might be affected in the mutated plants compared to the control.