20.109(F07):Module 2

Module 2
Instructors: Natalie Kuldell and Agi Stachowiak

TA: Alice Lo

In this experiment, we will consider unintended and unpredicted effects of an experimental perturbation. Our goal is a precise one, namely to silence gene expression of a measurable gene, luciferase, using RNA interference (RNAi). Each group will begin by designing a short interfering RNA (siRNA) against luciferase, but as we'll see, siRNAs can vary in efficacy and specificity. After transfecting a mammalian cell line with the siRNA you’ve designed and a reporter plasmid, we will evaluate the silencing using a luciferase assay and microarray technology. The first assay evaluates the efficacy of the siRNA in silencing. The second assay gives genome-wide expression data to reveal the specificity of your siRNA for the gene you’ve targeted. Through this combined approach, we'll assess the balance of targeted and off-target effects.

Module 2 Day 1: siRNA design and introduction to cell culture Module 2 Day 2: Transfection Module 2 Day 3: Luciferase assays and RNA prep Module 2 Day 4: Journal article discussion Module 2 Day 5: cDNA synthesis and microarray Module 2 Day 6: Microarray data analysis Module 2 Day 7: Reports due Module 2 Day 8: Oral Presentations direct link to writing assignment

TA notes, mod 2