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| − | | <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M2D9| Homework due]] <br> <font color=#B40404>[[20.109(S20):Journal club presentations (Day4 and 5)|'''Journal Club presentation due'''</font color>]] Sun, Apr 12 at 10 pm <br>[https://be20109s20.blogspot.com/ Blog post due] Mon, Apr 13 at 10 pm <br> | + | | <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M2D9| Homework due]] <br> [[20.109(S20):Journal club presentations (Day4 and 5)|<font color=#B40404>'''Journal Club presentation due'''</font color>]] Sun, Apr 12 at 10 pm <br>[https://be20109s20.blogspot.com/ Blog post due] Mon, Apr 13 at 10 pm <br> |
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Revision as of 19:34, 17 March 2020
20.109(S20): Laboratory Fundamentals of Biological Engineering
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
T/R prelab
WF Prelab
|
|
| 2
|
4
|
T/W Mar 17/18
|
|
Take care of yourselves!
|
|
| 2
|
5
|
R/F Mar 19/20
|
|
Take care of yourselves!
|
|
|
|
|
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
|
Review qPCR experiment and complete statistical analysis
|
Laboratory quiz
Homework due
Data summary revision due Sun, Apr 5 at 10 pm
Blog post due Mon, Apr 6 at 10 pm
|
| 2
|
8
|
T/W Apr 7/8
|
EF
|
Complete RNA-seq data analysis
|
Homework due
|
|
|
| 2
|
9
|
R/F Apr 9/10
|
NLL
|
|
Laboratory quiz
Homework due
Journal Club presentation due Sun, Apr 12 at 10 pm
Blog post due Mon, Apr 13 at 10 pm
|
| 3
|
1
|
T/W Apr 14/15
|
LM
|
Enrich candidate clones using fluorescence-activated cell sorter (FACS)
|
Homework due
|
| 3
|
2
|
R/F Apr 16/17
|
Comm Lab
|
Harvest candidate clones and prepare for sequencing
|
Homework due
|
|
|
|
T/W Apr 21/22
|
|
Patriots' day holiday
|
Research article due Mon, Apr 20 at 10 pm
Blog post due Tue, Apr 21 at 10 pm
|
| 3
|
3
|
R/F Apr 23/24
|
LM
|
Identify clones to characterize
|
Laboratory quiz
Homework due
|
|
|
|
T/W Apr 28/29
|
LM
|
Research proposal pitches, will be scheduled with each team during laboratory time
|
|
| 3
|
4
|
R/F Apr/May 30/1
|
LM
|
Characterize clone by titration using flow cytometry
|
Homework due
|
| 3
|
5
|
R/F May 5/6
|
LM
|
Analyze titration curves
|
Homework due
|
|
|
|
R/F May 7/8
|
|
Research proposal presentations, will be scheduled with each team during laboratory time
|
|
|
|
|
T May 12
|
|
Feedback and celebratory lunch, to be rescheduled
|
Mini-report due Mon, May 11 at 10 pm
Blog post due Tue, May 12 at 10 pm
|
