Module 2

Lecturers: Ernest Fraenkel and Noreen Lyell
Instructors: Noreen Lyell and Leslie McClain, and Becky Meyer
Research assistant: Anne Shen
TAs: Kevin Chung and Joe Kreitz
Lab manager: Hsinhwa Lee

Overview

In Module 2 you will use two RNA-seq data sets to assess the effect of drug treatment on mammalian cells. RNA-seq is used to measure the transcriptome of a population of cells. By identifying which genes are active in response to a treatment, insights can be gathered regarding the cellular response. Specifically, the drug treatment you will use in your experiment is etoposide. Etoposide is known to generate double strand breaks in DNA and is used in chemotherapy. You will apply etoposide to DLD-1 cells, which are a cell line that originated from the colon of a male patient with colorectal adenocarcinoma Dukes Type C. In addition, you will compare the transcriptome results of your experiment (DLD-1 cells treated with etoposide) to published data using a different cell line (A549 cells) that were also treated with etoposide.

An additional goal of Module 2 is for you to synthesize data from different experiments into a single story. More often that not, researchers reach conclusions using results gathered from more than one experimental approach. Multiple layers of support can bolster a conclusion as they eliminate biases that may exist in a particular method of analysis. Furthermore, for complex questions it may be necessary to include data from several approaches to provide a sufficient conclusion.