Difference between revisions of "20.109(S20): Spring 2020 schedule"

From Course Wiki
Jump to: navigation, search
Line 89: Line 89:
 
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
 
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
 
| [[20.109(S20):Prepare cells for RNA purification and practice RNA-seq data analysis methods (Day1)| Prepare cells for RNA purification and practice RNA-seq data analysis methods]]<br>
 
| [[20.109(S20):Prepare cells for RNA purification and practice RNA-seq data analysis methods (Day1)| Prepare cells for RNA purification and practice RNA-seq data analysis methods]]<br>
| [[20.109(S20):Homework#Due_M2D1| Homework due]]
+
| [[20.109(S20):Homework#Due_M2D1| Homework due]]<br> [[20.109(S20): Data Summary| <font color=#B40404>'''Data summary draft due'''</font color>]] Sun, Mar 8 at 10 pm<br>
 
|--
 
|--
 
| 2
 
| 2
Line 96: Line 96:
 
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
 
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
 
| [[20.109(S20):Treat cells with etoposide and analyze RNA-seq data (Day2)| Treat cells with etoposide and analyze RNA-seq data]]<br>
 
| [[20.109(S20):Treat cells with etoposide and analyze RNA-seq data (Day2)| Treat cells with etoposide and analyze RNA-seq data]]<br>
| [[20.109(S20):Homework#Due_M2D2| Homework due]]<br> [[20.109(S20): Data Summary| <font color=#B40404>'''Data summary draft due'''</font color>]] Sun, Mar 8 at 10 pm<br>
+
| [[20.109(S20):Homework#Due_M2D2| Homework due]]
 
|--
 
|--
 
| 2
 
| 2
Line 103: Line 103:
 
| [http://be.mit.edu/directory/ernest-fraenkel EF] <br>  
 
| [http://be.mit.edu/directory/ernest-fraenkel EF] <br>  
 
| [[20.109(S20):Purify RNA from etoposide-treated cells and and generate cDNA (Day3)| Purify RNA from etoposide-treated cells and generate cDNA]]<br>
 
| [[20.109(S20):Purify RNA from etoposide-treated cells and and generate cDNA (Day3)| Purify RNA from etoposide-treated cells and generate cDNA]]<br>
| [[20.109(S20):Homework#Due_M2D3| Homework due]] <br> [[20.109(S20): Mini-presentation| <font color=#B40404>'''Mini-presentation due'''</font color>]] Sun, Mar 15 at 10 pm<br>[https:// Blog post due] Mon, Mar 16 at 10 pm <br>
+
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M2D3| Homework due]] <br> [[20.109(S20): Mini-presentation| <font color=#B40404>'''Mini-presentation due'''</font color>]] Sun, Mar 15 at 10 pm<br>[https:// Blog post due] Mon, Mar 16 at 10 pm <br>
 
|--
 
|--
 
| 2
 
| 2
Line 117: Line 117:
 
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
 
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
 
| [[20.109(S20):Journal club presentations (Day4 and 5)| Journal club II presentations]]<br>
 
| [[20.109(S20):Journal club presentations (Day4 and 5)| Journal club II presentations]]<br>
|  
+
| [[20.109(S20): Data Summary| <font color=#B40404>'''Data summary revision due'''</font color>]] Sun, Mar 22 at 10 pm
 
|--
 
|--
 
|  
 
|  
Line 124: Line 124:
 
|   
 
|   
 
| <font color = #FACC2E>'''Spring vacation'''</font color>
 
| <font color = #FACC2E>'''Spring vacation'''</font color>
| [[20.109(S20): Data Summary| <font color=#B40404>'''Data summary revision due'''</font color>]] Sun, Mar 22 at 10 pm
+
|  
 
|--
 
|--
 
|  
 
|  
Line 138: Line 138:
 
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
 
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
 
| [[20.109(S20):Analyze RNA-seq data and select gene targets for quantitative PCR (qPCR) experiment (Day 6)| Analyze RNA-seq data and select gene targets for quantitative PCR experiment]]<br>
 
| [[20.109(S20):Analyze RNA-seq data and select gene targets for quantitative PCR (qPCR) experiment (Day 6)| Analyze RNA-seq data and select gene targets for quantitative PCR experiment]]<br>
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M2D6| Homework due]]  
+
| [[20.109(S20):Homework#Due_M2D6| Homework due]]  
 
|--
 
|--
 
| 2
 
| 2
Line 189: Line 189:
 
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>
 
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>
 
| [[20.109(S20): (Day4)| ]]<br>
 
| [[20.109(S20): (Day4)| ]]<br>
| [[20.109(S20):Homework#Due_M3D3| Homework due]]
+
| [[20.109(S20):Homework#Due_M3D4| Homework due]]
 
|--
 
|--
 
|  
 
|  
Line 203: Line 203:
 
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>
 
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>
 
| [[20.109(S20): (Day5)| ]]<br>
 
| [[20.109(S20): (Day5)| ]]<br>
| [[20.109(S20):Homework#Due_M3D4| Homework due]]
+
| [[20.109(S20):Homework#Due_M3D5| Homework due]]
 
|--
 
|--
 
| 3
 
| 3
Line 210: Line 210:
 
| [http://be.mit.edu/directory/leslie-mcclain LM]
 
| [http://be.mit.edu/directory/leslie-mcclain LM]
 
| [[20.109(S20): (Day6) | ]]<br>
 
| [[20.109(S20): (Day6) | ]]<br>
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M3D5| Homework due]]
+
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M3D6| Homework due]]
 
|--
 
|--
 
|  
 
|  
Line 224: Line 224:
 
|  
 
|  
 
| <font color = #FACC2E>'''Feedback and celebratory lunch'''</font color>
 
| <font color = #FACC2E>'''Feedback and celebratory lunch'''</font color>
| [[20.109(S20): Mini-report | <font color=#B40404>'''Mini-report due'''</font color>]] Tue, May 12 at 10 pm <br>
+
| [[20.109(S20): Mini-report | <font color=#B40404>'''Mini-report due'''</font color>]] Mon, May 11 at 10 pm <br>
 
|}
 
|}
 
</div>
 
</div>

Revision as of 21:15, 16 January 2020

20.109(S20): Laboratory Fundamentals of Biological Engineering

Sp20 banner image v2.png

Spring 2020 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Screening ligand binding        2. Measuring gene expression        3. Engineering antibodies              


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 and laboratory tour
1 1 R/F Feb 6/7 AK
Complete in silico cloning and induce TDP43 protein expression
Orientation quiz
Homework due
1 2 T/W Feb 11/12 AK
Purify TDP43 protein
Homework due
1 3 R/F Feb 13/14 AK
Assess purity and concentration of TDP43 protein
Homework due
T/W Feb 18/19 President's day holiday
1 4 R/F Feb 20/21 AK
Perform small molecule microarray (SMM) with TDP43 protein
Laboratory quiz
Homework due
1 5 T/W Feb 25/26 AK
Scan SMM slides to identify binders of TDP43 protein
Homework due
1 6 R/F Feb 27/28 AK
Analyze SMM data
Homework due
1 7 T/W Mar 3/4 AK
Examine TDP43 binders for chemical features
Laboratory quiz
Homework due
2 1 R/F Mar 5/6 NLL
Prepare cells for RNA purification and practice RNA-seq data analysis methods
Homework due
Data summary draft due Sun, Mar 8 at 10 pm
2 2 T/W Mar 10/11 EF
Treat cells with etoposide and analyze RNA-seq data
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
[https:// 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
Sort antibody library using fluorescence-activated cell sorter (FACS)
Homework due
3 2 T/W Apr 14/15 Comm Lab

Homework due
3 3 R/F Apr 16/17 LM

Laboratory quiz
Homework due
Research article due Sun, Apr 19 at 10 pm
[https:// 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

Homework due
T/W Apr 28/29 Research proposal pitches in lecture, no laboratory
3 5 R/F Apr/May 30/1 LM

Homework due
3 6 T/W May 5/6 LM
Laboratory quiz
Homework due
R/F May 7/8 Research proposal presentations [https:// 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