Difference between revisions of "20.109(F19): Fall 2019 schedule"
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| T/W Sept 17/18 | | T/W Sept 17/18 | ||
| [http://be.mit.edu/directory/bevin-p-engelward BE] | | [http://be.mit.edu/directory/bevin-p-engelward BE] | ||
| − | | [[20.109(F19):Complete gamma-H2AX assay and prepare CometChip (Day3)| Perform immunofluorescence assay for repair foci and optimize high-throughput genome damage assay]]<br> | + | | [[20.109(F19):Complete gamma-H2AX assay and prepare CometChip (Day3)| Perform immunofluorescence assay for repair foci and optimize high-throughput genome damage assay]]<br>[[Media:M1D3_Fa19_LMmarked.pdf| Prelab T/R]] <br> [[Media:M1D3 Fa19 bcm marked.pdf| Prelab W/F]] |
| [[20.109(F19):Homework#Due_M1D3|Homework due]] | | [[20.109(F19):Homework#Due_M1D3|Homework due]] | ||
|-- | |-- | ||
| Line 58: | Line 58: | ||
| T/W Sept 24/25 | | T/W Sept 24/25 | ||
| [http://be.mit.edu/directory/bevin-p-engelward BE] | | [http://be.mit.edu/directory/bevin-p-engelward BE] | ||
| − | | [[20.109(F19):Load cells into CometChip and apply treatments (Day4)| Perform immunofluorescence imaging for repair foci and expose cells for high-throughput genome damage assay]]<br> | + | | [[20.109(F19):Load cells into CometChip and apply treatments (Day4)| Perform immunofluorescence imaging for repair foci and expose cells for high-throughput genome damage assay]]<br>[[Media:M1D4_Fa19_LMmarked.pdf| Prelab T/R]] <br> [[Media:M1D4 Fa19 bcm marked.pdf|Prelab W/F]] |
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M1D4|Homework due]] | | <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M1D4|Homework due]] | ||
|-- | |-- | ||
| Line 65: | Line 65: | ||
| R/F Sept 26/27 | | R/F Sept 26/27 | ||
| [http://be.mit.edu/directory/bevin-p-engelward BE] | | [http://be.mit.edu/directory/bevin-p-engelward BE] | ||
| − | | [[20.109(F19):Complete CometChip experiment (Day5)| Quantify repair foci via network algorithm and complete high-throughput genome damage assay]]<br> | + | | [[20.109(F19):Complete CometChip experiment (Day5)| Quantify repair foci via network algorithm and complete high-throughput genome damage assay]]<br>[[Media:Fa19 M1D5 Dushan ver2.pdf|Dushan's Talk]]<br>[[Media:M1D5_Fa19_LMmarked.pdf|TR Prelab]] <br> [[Media:M1D5 Fa19 bcm.pdf | WF Prelab]] |
| [[20.109(F19):Homework#Due_M1D5|Homework due]] | | [[20.109(F19):Homework#Due_M1D5|Homework due]] | ||
|-- | |-- | ||
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| T/W Oct 1/2 | | T/W Oct 1/2 | ||
| [http://be.mit.edu/directory/bevin-p-engelward BE] | | [http://be.mit.edu/directory/bevin-p-engelward BE] | ||
| − | | [[20.109(F19):Image CometChip (Day6)| Perform quantitative image analysis for the high-throughput genome damage assay]]<br> | + | | [[20.109(F19):Image CometChip (Day6)| Perform quantitative image analysis for the high-throughput genome damage assay]]<br>[[Media:M1D6_Fa19_LMmarked.pdf|TR Prelab]] <br> [[Media:M1D6 Fa19 bcm marked.pdf | WF Prelab]] |
| [[20.109(F19):Homework#Due_M1D6|Homework due]] | | [[20.109(F19):Homework#Due_M1D6|Homework due]] | ||
|-- | |-- | ||
| Line 79: | Line 79: | ||
| R/F Oct 3/4 | | R/F Oct 3/4 | ||
| [http://be.mit.edu/directory/bevin-p-engelward BE] | | [http://be.mit.edu/directory/bevin-p-engelward BE] | ||
| − | | [[20.109(F19):Practice statistical analysis methods and complete data analysis (Day7)| Complete data analysis and apply statistical methods]]<br> | + | | [[20.109(F19):Practice statistical analysis methods and complete data analysis (Day7)| Complete data analysis and apply statistical methods]]<br>[[Media:M1D7_Fa19_LMmarked.pdf|TR Prelab]] <br> [[Media:M1D7 Fa19 bcm.pdf | WF Prelab]] |
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M1D7|Homework due]] | | <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M1D7|Homework due]] | ||
|-- | |-- | ||
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| 1 | | 1 | ||
| T/W Oct 8/9 | | T/W Oct 8/9 | ||
| − | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D1 lecture slides v2.pdf| Lecture slides]] |
| − | | [[20.109(F19):Complete in silico cloning of pdCas9 (Day1)| Complete in silico cloning of pdCas9]]<br> | + | | [[20.109(F19):Complete in silico cloning of pdCas9 (Day1)| Complete in silico cloning of pdCas9]]<br>[[Media:M2D1_Fa19_LMmarked.pdf|TR Prelab]]<br> [[Media:M2D1 Fa19 bcm marked.pdf | WF Prelab]] |
| [[20.109(F19):Homework#Due_M2D1| Homework due]]<br> | | [[20.109(F19):Homework#Due_M2D1| Homework due]]<br> | ||
|-- | |-- | ||
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| 2 | | 2 | ||
| R/F Oct 10/11 | | R/F Oct 10/11 | ||
| − | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D2 lecture slides v2.pdf|Lecture slides]] |
| − | | [[20.109(F19):Design gRNA sequence for CRISPRi (Day2)| Design gRNA sequence for CRISPRi]]<br> | + | | [[20.109(F19):Design gRNA sequence for CRISPRi (Day2)| Design gRNA sequence for CRISPRi]]<br>[[Media:M2D2_Fa18_SPmarked.pdf|TR Prelab]]<br>[[Media:Fa19 M2D2 CYK marked.pdf|WF Prelab]] |
| [[20.109(F19):Homework#Due_M2D2|Homework due]] | | [[20.109(F19):Homework#Due_M2D2|Homework due]] | ||
|-- | |-- | ||
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| | | | ||
| <font color = 999999>Columbus day holiday</font color> | | <font color = 999999>Columbus day holiday</font color> | ||
| − | | [[20.109(F19): Data Summary| Data Summary draft due]] Mon, Oct 14 at 10 pm<br>[ Blog post due] | + | | [[20.109(F19): Data Summary| Data Summary draft due]] Mon, Oct 14 at 10 pm<br>[https://be20109f19.blogspot.com/ Blog post due] Fri, Oct 18 at 10 pm |
|-- | |-- | ||
| colspan="7" | | | colspan="7" | | ||
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| 3 | | 3 | ||
| R/F Oct 17/18 | | R/F Oct 17/18 | ||
| − | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa18 M2D3 figures.pptx| Article Figures]]<br>[[Media:Fa19 M2D3 paper discussion slides.pdf| Lecture slides]] |
| − | | [[20.109(F19):Generate gRNA plasmid (Day3)| Generate gRNA plasmid]]<br> | + | | [[20.109(F19):Generate gRNA plasmid (Day3)| Generate gRNA plasmid]]<br> [[Media:M2D3_Fa18_LM_SP_edit.pdf | TR Prelab]]<br> [[Media:Fa19 M2D3 bcm marked.pdf | WF Prelab]] |
| [[20.109(F19):Homework#Due_M2D3|Homework due]]<br>[[20.109(F19): Mini-presentation| Mini-presentation due]] Sat, Oct 19 at 10 pm | | [[20.109(F19):Homework#Due_M2D3|Homework due]]<br>[[20.109(F19): Mini-presentation| Mini-presentation due]] Sat, Oct 19 at 10 pm | ||
|-- | |-- | ||
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| 4 | | 4 | ||
| T/W Oct 22/23 | | T/W Oct 22/23 | ||
| − | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D4 lecture slides.pdf|Lecture slides]] |
| [[20.109(F19):Journal club presentation (Day4 and 6)| Journal club I]] | | [[20.109(F19):Journal club presentation (Day4 and 6)| Journal club I]] | ||
| | | | ||
| Line 122: | Line 122: | ||
| 5 | | 5 | ||
| R/F Oct 24/25 | | R/F Oct 24/25 | ||
| − | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D5 lecture slides v2.pdf| Lecture slides]] |
| − | | [[20.109(F19):Confirm gRNA sequence in pgRNA (Day5)| Confirm gRNA sequence in pgRNA]]<br> | + | | [[20.109(F19):Confirm gRNA sequence in pgRNA (Day5)| Confirm gRNA sequence in pgRNA]]<br> [[Media: M2D5_Fa19_LMmarked.pdf | TR Prelab]]<br> [[Media:Fa19 M2D5 cyk marked.pdf | WF Prelab]] |
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M2D5|Homework due]]<br>[[20.109(F19): Data Summary| Data Summary revision due]] Sat, Oct 26 at 10 pm | | <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M2D5|Homework due]]<br>[[20.109(F19): Data Summary| Data Summary revision due]] Sat, Oct 26 at 10 pm | ||
|-- | |-- | ||
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| 6 | | 6 | ||
| T/W Oct 29/30 | | T/W Oct 29/30 | ||
| − | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D6 lecture slides.pdf|Lecture slides]] |
| [[20.109(F19):Journal club presentation (Day4 and 6) | Journal club II]] | | [[20.109(F19):Journal club presentation (Day4 and 6) | Journal club II]] | ||
| | | | ||
| Line 136: | Line 136: | ||
| 7 | | 7 | ||
| R/F Oct/Nov 31/1 | | R/F Oct/Nov 31/1 | ||
| − | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D7 lecture slides.pdf| Lecture slides]] |
| − | | [[20.109(F19):Induce CRISPRi system (Day7)| Induce CRISPRi system]]<br> | + | | [[20.109(F19):Induce CRISPRi system (Day7)| Induce CRISPRi system]]<br> [[Media: M2D7_Fa19_LM.pdf | TR Prelab]] <br> [[Media:Fa18 M2D7 bcm marked.pdf | WF Prelab]] |
| − | | [[20.109(F19):Homework#Due_M2D7|Homework due]]<br>[ Blog post due] Fri, Nov 1 at 10 pm | + | | [[20.109(F19):Homework#Due_M2D7|Homework due]]<br>[https://be20109f19.blogspot.com/ Blog post due] Fri, Nov 1 at 10 pm |
|-- | |-- | ||
| 2 | | 2 | ||
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| T/W Nov 5/6 | | T/W Nov 5/6 | ||
| [http://be.mit.edu/directory/noreen-lyell NLL]<br> | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | ||
| − | | [[20.109(F19):Measure_fermentation_products_(Day8) | Measure fermentation products]]<br> | + | | [[20.109(F19):Measure_fermentation_products_(Day8) | Measure fermentation products]]<br> [[Media: M2D8_Fa19_LMmarked.pdf | TR Prelab]] <br> [[Media:Fa19 M2D8 bcm marked.pdf | WF Prelab]] |
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M2D8|Homework due]] | | <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M2D8|Homework due]] | ||
|-- | |-- | ||
| Line 152: | Line 152: | ||
| 1 | | 1 | ||
| R/F Nov 7/8 | | R/F Nov 7/8 | ||
| − | | [https://be.mit.edu/directory/angela-koehler AK]<br> | + | | [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L1 2019.pptx|Lecture slides]] |
| − | | [[20.109(F19):Prepare for cellular thermal shift assay (Day1)| Prepare for cellular thermal shift assay]]<br> | + | | [[20.109(F19):Prepare for cellular thermal shift assay (Day1)| Prepare for cellular thermal shift assay]]<br> [[Media:Fa19 M3D1 prelab slides nllmarked.pdf| TR Prelab]] <br> [[Media:Fa19 M3D1 bcm marked.pdf | WF Prelab]] |
| [[20.109(F19):Homework#Due_M3D1|Homework due]] <br> | | [[20.109(F19):Homework#Due_M3D1|Homework due]] <br> | ||
|-- | |-- | ||
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| | | | ||
| <font color = 999999>Veterans' day holiday</font color> | | <font color = 999999>Veterans' day holiday</font color> | ||
| − | | [[20.109(F19): Research article| Research article due]] Mon, Nov 11 at 10 pm <br>[ Blog post due] Tue, Nov 12 at 10 pm | + | | [[20.109(F19): Research article| Research article due]] Mon, Nov 11 at 10 pm <br>[https://be20109f19.blogspot.com/ Blog post due] Tue, Nov 12 at 10 pm |
|-- | |-- | ||
| 3 | | 3 | ||
| 2 | | 2 | ||
| R/F Nov 14/15 | | R/F Nov 14/15 | ||
| − | | [https://be.mit.edu/directory/angela-koehler AK]<br> | + | | [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L2 2019.pptx|Lecture slides]] |
| − | | [[20.109(F19):Incubate with ligand and apply heat treatment for protein denaturation (Day2)| Incubate with ligand and apply heat treatment for protein denaturation]]<br> | + | | [[20.109(F19):Incubate with ligand and apply heat treatment for protein denaturation (Day2)| Incubate with ligand and apply heat treatment for protein denaturation]]<br>[[Media:Fa19 M3D2 prelab slides nllmarked.pdf|TR Prelab]] <br> [[Media:191115 prelab CYK marked.pdf | WF Prelab]] |
| [[20.109(F19):Homework#Due_M3D2|Homework due]]<br> | | [[20.109(F19):Homework#Due_M3D2|Homework due]]<br> | ||
|-- | |-- | ||
| Line 173: | Line 173: | ||
| 3 | | 3 | ||
| T/W Nov 19/20 | | T/W Nov 19/20 | ||
| − | | [https://be.mit.edu/directory/angela-koehler AK]<br> | + | | [https://be.mit.edu/directory/angela-koehler AK]<br> [[Media:20109 Struntz Lecture 2019.pdf| Lecture slides]] |
| − | | [[20.109(F19):Begin Western blot analysis (Day3)| Begin Western blot analysis]]<br> | + | | [[20.109(F19):Begin Western blot analysis (Day3)| Begin Western blot analysis]]<br>[[Media:Fa19 M3D3 prelab slides nllmarked.pdf|TR Prelab]] <br> [[Media:Fa19 M3D3 bcm.pdf | WF Prelab]] |
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M3D3| Homework due]] | | <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M3D3| Homework due]] | ||
|-- | |-- | ||
| Line 180: | Line 180: | ||
| 4 | | 4 | ||
| R/F Nov 21/22 | | R/F Nov 21/22 | ||
| − | | [https://be.mit.edu/directory/angela-koehler AK]<br> | + | | [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L4 2019.pdf| Lecture slides]] |
| − | | [[20.109(F19):Complete antibody staining for Western blot analysis (Day4)| Complete antibody staining for Western blot analysis]]<br> | + | | [[20.109(F19):Complete antibody staining for Western blot analysis (Day4)| Complete antibody staining for Western blot analysis]]<br> [[Media:M3D4 Fa19 bcm marked.pdf | TR Prelab]] <br> [[Media:M3D4WF Fa19 bcm marked.pdf | WF Prelab]] |
| [[20.109(F19):Homework#Due_M3D4|Homework due]] | | [[20.109(F19):Homework#Due_M3D4|Homework due]] | ||
|-- | |-- | ||
| Line 188: | Line 188: | ||
| T/W Nov 26/27 | | T/W Nov 26/27 | ||
| | | | ||
| − | | <font color = #0101DF>'''Lecture, but no laboratory'''</font color> | + | | <font color = #0101DF>'''Lecture: research proposal pitch, but no laboratory'''</font color> |
| | | | ||
|-- | |-- | ||
| Line 201: | Line 201: | ||
| 5 | | 5 | ||
| T/W Dec 3/4 | | T/W Dec 3/4 | ||
| − | | [https://be.mit.edu/directory/angela-koehler AK]<br> | + | | [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L5 2019.pdf| Lecture slides]] |
| − | | [[20.109(F19):Data analysis and assignment preparation (Day5)| Data analysis and assignment preparation]]<br> | + | | [[20.109(F19):Data analysis and assignment preparation (Day5)| Data analysis and assignment preparation]]<br>[[Media:Fa19 M3D5 prelab slides nllmarked.pdf| TR Prelab]] <br> [[Media:Fa19 M3D5 bcm marked.pdf | WF Prelab]] |
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M3D5|Homework due]] | | <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M3D5|Homework due]] | ||
|-- | |-- | ||
| Line 210: | Line 210: | ||
| | | | ||
| [[20.109(F19):Research proposal presentation| Research proposal presentations]] | | [[20.109(F19):Research proposal presentation| Research proposal presentations]] | ||
| − | | [ Blog post due] Fri, Dec 6 at 10 pm | + | | [https://be20109f19.blogspot.com/ Blog post due] Fri, Dec 6 at 10 pm |
|-- | |-- | ||
| colspan="7" | | | colspan="7" | | ||
Latest revision as of 19:19, 4 December 2019
Welcome to 20.109! It is our goal to make this class a useful and fun introduction to the experiments and techniques used 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 (16-220)
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)
