20.109(F07):Module 2: Difference between revisions
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[[20.109(F07): Mod 2 Day 7| Module 2 Day 7: Reports due]]<br> | [[20.109(F07): Mod 2 Day 7| Module 2 Day 7: Reports due]]<br> | ||
[[20.109(F07): Module 2 oral presentations| Module 2 Day 8: Oral Presentations]]<br> | [[20.109(F07): Module 2 oral presentations| Module 2 Day 8: Oral Presentations]]<br> | ||
direct link to [[20.109(F07): Expression engineering report| writing assignment]]<br> | |||
[[20.109(F07): TA's notes for module 2| TA notes, mod 2]] | [[20.109(F07): TA's notes for module 2| TA notes, mod 2]] | ||
Latest revision as of 07:11, 2 September 2007
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
