20.109(S20): Spring 2020 schedule

Welcome to 20.109! It is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. Though there is not time enough to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.

SCHEDULE DETAILS:
Lecture times: T/R 11 - 12 pm (56-154)
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)

MODULE	DAY	DATE	LECTURER	LABORATORY EXPERIMENTS	ASSIGNMENTS
		T/W Feb 4/5	NLL Orientation lecture	Orientation and laboratory tour Lab Orientation Prelab
1	1	R/F Feb 6/7	AK M1D1 lecture	Complete in silico cloning and induce TDP43 protein expression T/R prelab WF Prelab	Orientation quiz Homework due
1	2	T/W Feb 11/12	AK M1D2 lecture	Purify TDP43 protein T/R prelab W/F prelab	Homework due
1	3	R/F Feb 13/14	AK M1D3 lecture	Assess purity and concentration of TDP43 protein T/R prelab WF Prelab	Homework due
		T/W Feb 18/19		President's day holiday
1	4	R/F Feb 20/21	AK M1D4 lecture	Perform small molecule microarray (SMM) with TDP43 protein T/R prelab WF prelab	Laboratory quiz Homework due
1	5	T/W Feb 25/26	AK M1D5 lecture	Scan SMM slides to identify binders of TDP43 protein T/R prelab WF prelab	Homework due
1	6	R/F Feb 27/28	AK M1D6 lecture	Analyze SMM data T/R Prelab WF Prelab	Homework due
1	7	T/W Mar 3/4	AK M1D7 lecture	Examine TDP43 binders for chemical features T/R prelab WF Prelab	Laboratory quiz Homework due
2	1	R/F Mar 5/6	NLL M2D1 lecture	Prepare cells for RNA purification and practice RNA-seq data analysis methods T/R prelab W/F prelab	Homework due Data summary draft due Sun, Mar 8 at 10 pm
2	2	T/W Mar 10/11	EF M2D2 lecture	Treat cells with etoposide and analyze RNA-seq data T/R prelab WF Prelab	Homework due
2	3	R/F Mar 12/13	EF	Purify RNA from etoposide-treated cells and generate cDNA	Laboratory quiz Homework due Mini-presentation due Sun, Mar 15 at 10 pm Blog post due Mon, Mar 16 at 10 pm
2	4	T/W Mar 17/18	EF	Journal club I presentations
2	5	R/F Mar 19/20	EF	Journal club II presentations	Data summary revision due Sun, Mar 22 at 10 pm
		T/W Mar 24/25		Spring vacation
		R/F Mar 26/27		Spring vacation
2	6	T/W Mar/Apr 31/1	EF	Analyze RNA-seq data and select gene targets for quantitative PCR experiment	Homework due
2	7	R/F Apr 2/3	EF	Perform qPCR experiment and continue RNA-seq data analysis	Homework due
2	8	T/W Apr 7/8	NLL	Examine qPCR results and complete data analysis	Laboratory quiz Homework due
3	1	R/F Apr 9/10	LM	Enrich candidate clones using fluorescence-activated cell sorter (FACS)	Homework due
3	2	T/W Apr 14/15	Comm Lab	Harvest candidate clones	Homework due
3	3	R/F Apr 16/17	LM	Prepare clones for sequencing	Laboratory quiz Homework due Research article due Sun, Apr 19 at 10 pm Blog post due Mon, Apr 20 at 10 pm
		T/W Apr 21/22		Patriots' day holiday
3	4	T/W Apr 23/24	LM	Identify clone to characterize	Homework due
		T/W Apr 28/29		Research proposal pitches in lecture, no laboratory
3	5	R/F Apr/May 30/1	LM	Characterize clone by titration using flow cytometry	Homework due
3	6	T/W May 5/6	LM	Analyze titration curves	Laboratory quiz Homework due
		R/F May 7/8		Research proposal presentations	Blog post due Sat, May 9 at 10 pm
		T May 12		Feedback and celebratory lunch	Mini-report due Mon, May 11 at 10 pm Blog post due Tue, May 12 at 10 pm