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Team:UNIPV-Pavia/Notebook/Week2
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*NOTES: to avoid smearing fragments during electrophoresis, we planned experiments in which only excided fragments of the same order of magnitude are ran in the same gel. So, we decided to run these four parts on May 28 (the smaller part is 660 bp and the larger one is 1128 bp). The remaining parts will be digested/gel extracted on May 29 (the smaller part is 39 bp and the larger one is 157 bp). | *NOTES: to avoid smearing fragments during electrophoresis, we planned experiments in which only excided fragments of the same order of magnitude are ran in the same gel. So, we decided to run these four parts on May 28 (the smaller part is 660 bp and the larger one is 1128 bp). The remaining parts will be digested/gel extracted on May 29 (the smaller part is 39 bp and the larger one is 157 bp). | ||
| - | *BBa_J23100 9 ml culture grown overnight was not red as we expected! So we performed miniprep only for BBa_B0030 9 ml culture, after taking 800 µl | + | *BBa_J23100 9 ml culture grown overnight was not red as we expected! So we performed miniprep only for BBa_B0030 9 ml culture, after taking 800 µl from 9 ml BBa_B0030 culture to prepare a new glycerol stock. |
*Unfortunately DNA pellet wash failed...Unlucky day for miniprep! | *Unfortunately DNA pellet wash failed...Unlucky day for miniprep! | ||
*We took 15 µl again from BBa_B0030 and BBa_J23100 glycerol stocks and infected 9 ml LB + Amp for each part. We incubated the 9 ml cultures at 37°C overnight. | *We took 15 µl again from BBa_B0030 and BBa_J23100 glycerol stocks and infected 9 ml LB + Amp for each part. We incubated the 9 ml cultures at 37°C overnight. | ||
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| + | '''05/29/08''' | ||
| + | <br> | ||
| + | *9 ml cultures were grown correctly and BBa_J23100 culture was red. So we could perform miniprep for these 2 parts. | ||
Revision as of 19:49, 29 May 2008
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Notebook
| Week 1 | Week 2 |
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Week 2: 05/26/08 - 05/29/08
05/26/08
- Team meeting at Biomedical Informatics Lab to talk about UNIPV-Pavia team presentation at Paris Teacher's Workshop and to make our first wiki updating.
- We received restriction enzymes and Agarose Gel DNA Extraction Kit from Roche. Now we are ready to cut;)
05/27/08
- We performed plasmid digestion for these 9 parts (1 µg):
| BBa_C0078 (X-P) | BBa_E0040 (X-P) | BBa_E1010 (X-P) | BBa_C0051 (X-P) |
| BBa_B0030 (X-P) | BBa_B0030 (E-X) | BBa_B0030 (S-P) | BBa_E0240 (E-X) |
| BBa_J23100 (E-S) |
- We had to insulate excided fragments for:
| BBa_C0078 (X-P) | BBa_E0040 (X-P) | BBa_E1010 (X-P) | BBa_C0051 (X-P) |
| BBa_B0030 (X-P) | BBa_J23100 (E-S) |
- While we had to insulate opened plasmids for:
| BBa_B0030 (E-X) | BBa_B0030 (S-P) | BBa_E0240 (E-X) |
- We ran two different gels for these two groups, because excided fragments are smaller then opened plasmids.
- Unfortunately, BBa_B0030 (X-P) and BBa_J23100 (E-S) fragments had smearing appearance because they were smaller then other excided fragments and ran too fast.
- We performed gel extraction for all the 9 parts, but we decided to repeat cutting/run/extraction process for BBa_B0030 (X-P) and BBa_J23100 (E-S) in the next days, to perform a more efficient extraction for these 2 parts.
- We took 15 µl from BBa_B0030 and BBa_J23100 glycerol stocks and infected 9 ml LB + Amp for each part. We incubated the 9 ml cultures at 37°C overnight. (We already had at our disposal extracted plasmids for these 2 parts, but we performed plasmid extraction anyway to have more).
05/28/08
- We performed plasmid digestion for these 4 parts (about 5.5 µg for BBa_C0062; the whole quantity for others):
| BBa_C0062 (X-P) | BBa_C0012 (X-P) | BBa_C0040 (X-P) | BBa_I15009 (X-P) |
- NOTES: to avoid smearing fragments during electrophoresis, we planned experiments in which only excided fragments of the same order of magnitude are ran in the same gel. So, we decided to run these four parts on May 28 (the smaller part is 660 bp and the larger one is 1128 bp). The remaining parts will be digested/gel extracted on May 29 (the smaller part is 39 bp and the larger one is 157 bp).
- BBa_J23100 9 ml culture grown overnight was not red as we expected! So we performed miniprep only for BBa_B0030 9 ml culture, after taking 800 µl from 9 ml BBa_B0030 culture to prepare a new glycerol stock.
- Unfortunately DNA pellet wash failed...Unlucky day for miniprep!
- We took 15 µl again from BBa_B0030 and BBa_J23100 glycerol stocks and infected 9 ml LB + Amp for each part. We incubated the 9 ml cultures at 37°C overnight.
05/29/08
- 9 ml cultures were grown correctly and BBa_J23100 culture was red. So we could perform miniprep for these 2 parts.
