20.109(S09): Expression engineering report

Overview
The culminating assignment for Module 2 will be a condensed research article in which you describe your expression engineering investigation. The target audience for this report is someone who is intimately familiar with your research and wants a status report, such as a research advisor. You can assume that she is familiar with most of the topics you would normally cover in an introduction section, and also already has access to your methods information. Thus, you are free to spend almost all your time developing a carefully analyzed results section and a thoughtful discussion.

Collaboration and Integrity
This report must be written entirely by you. Thus, while we encourage you to discuss your results with your lab partner and other classmates, you may not share text or figures. Please do not plagiarize (accidentally or otherwise) the class wiki, or any other writing/images available online or elsewhere.

In order for you to have the best learning experience possible, and to maintain a fair playing field for all students in the class, we ask that you do not look at completed assignments for similar modules run in previous years.

Method of Submission
Please email your completed report to 20109 DOT submit AT gmail DOT com, with filename Firstinitial_Lastname_LabSection_Mod2.doc (for example, S_Hockfield_TR_Mod2.doc).

First Draft Submission: April 14th/15th
The first draft of your research article is due by 11 am on April 14th (Tuesday) or April 15th (Wednesday), according to which day you have lab. Update: The first draft is due by midnight on April 15th (Wednesday) or April 16th (Thursday), respectively (i.e., about 1.5 days later than the initial date).

Revised Article Submission: April 30th/May 1st
Your first draft, with feedback from both the writing and the technical faculty, will be returned on April 23rd (Thursday) or 24th (Friday). You will then have the opportunity to revise your report for up to a one letter grade improvement. The final draft is due on April 30th (Thursday) or May 1st (Friday), according to which day you have lab.

Formatting Expectations

 * Your main document (excluding figures) should be/have
 * .doc (preferred) or .pdf
 * 12-pt font
 * with 1-inch margins
 * double-spaced (excepting the abstract)
 * Figures can be made in a separate drawing program (such as powerpoint), and should be submitted as .pdf

Guidelines on Length
Not counting figures or appendix, report length should not exceed 10 pages.

Abstract
You should write an abstract for this assignment, according to Module 1 guidelines.

Introduction
This condensed report will have only a brief introduction section, just to make sure that you and your advisor are on the same page, and that she knows the focus of your present investigation. Please limit it to one paragraph. For examples of condensed, investigation-oriented introductions, look at the letters section of Nature magazine. The paper that we read and discussed on Day 2, about small activating RNA, also has a concise, streamlined introduction.

Materials and Methods
Assume that your advisor already has access to all your protocols on your well-kept lab wiki, and omit this section :)

Results
The expectations for this part of the assignment are identical to those in Module 1.

Discussion
This section should realize all the good practices described in the Module 1 assignment, but do so at a more advanced level. You will be expected to cite the broader scientific literature more thoroughly than before, to propose specific future experiments, and to otherwise show that you deeply understand the meaning and significance of your results. In addition to drawing conclusions from your own data, you are expected to spend some time considering your classmates’ data, for both your own and for alternative siRNAs.

Suggested Figures
Your report is expected to contain more or less the following figures. Of course you are welcome to make modifications and additions as you see fit.


 * Table: siRNA experimental and control sequences
 * Figures
 * Luciferase data
 * Transfected cell images
 * Micrarray analysis workflow
 * Microarray results (likely to be multiple figures and tables)

Optional: Appendix
If you would like to give more details about your data analysis than you can clearly and concisely do in your main text, you may do so in an appendix.