Team:UNIPV-Pavia/Notebook/Week1Sep
From 2009.igem.org
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===== pH sensor ===== | ===== pH sensor ===== | ||
- | *We | + | *We streaked a single colony LB + Amp agar plate using K116002 glycerol stock. We incubated the plate at 37°C overnight. |
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*Preparation of LBK (LB with potassium instead of sodium) at pH 5,5 - 6,6 - 7,5 - 8,5 for the first experiment we would have performed in the following days. | *Preparation of LBK (LB with potassium instead of sodium) at pH 5,5 - 6,6 - 7,5 - 8,5 for the first experiment we would have performed in the following days. | ||
Revision as of 22:16, 13 October 2009
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Week from August 31st, to September 6th, 2009
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August, 31st
- We inoculated:
- 10 colonies from B5new2 plate in 4 ml of LB + Kan for screening;
- B8-5 (8 ul from glycerol stock) in 4 ml of LB + Kan (for purification process);
- We sent A15-2 purified DNA (stored at -20°C) to BMR Genomics for sequencing.
Experiment with Tecan F200
- Description
- Purpose:
- Materials & Methods
- Protocol
- Results
September, 1st
- We received sequencing results for:
- A16-4: sequence ok!
- A14-3: sequence had a deletion in C0012, as we expected because of A11-2 sequencing results, previously received;
- B8-5: sequence wrong in VF2 and good in VR;
- A17: chromatogram was good, but ligation failed (R0011 was not in the insert).
- COMMENTS after sequencing results:
- now we have a new aTc sensor (A16) to test together with A9;
- B8 has to be repeated or purified, we will try both the approaches;
- A14 has to be repeated using A11-3, which has a consistent sequencing result;
- A17 is going to be ligated today (this time using gel extraction).
- Glycerol stocks for the 10 B5new2 grown cultures.
- Miniprep for B5new2 (10 samples) and for B8-5.
- Digestion for:
- B5new2 (10 samples) for screening (E-P cut);
- B8-5 for purification from gel (E-P cut);
- R0011 (stored at -20°C) for A17new ligation (S-P cut)
- E0240 (stored at -20°C) for A17new ligation (X-P cut)
- Medium-size gel for B5new2(E-P); small-size gel for B8-5(E-P), R0011(S-P) and E0240(X-P).
- Medium gel results: B5new2 clones all showed the correct length for ligated plasmid! we decided to keep B5new2-3 to continue the assemblies and B5new2-9 as a backup copy. Both plasmids were sent to BMR Genomics for sequencing.
- Small gel results: R0011(S-P) and E0240(X-P) were cut and purified through gel-extraction, while B8-5 could not be cut because the bands were not correct: maybe the heaviest band noticed on August 24th was a non-completely digested fragment, not a correct-size insert. We decided to throw B8-5 glycerol stock away.
- Ligation: A17new = R0011(S-P) + E0240(X-P) in pSB1A2
- We incubated ligation reaction at 16°C overnight.
- We inoculated:
- B5new2-3
- B6-3
- A4
- F2620MIT1
- A11-3
pH sensor
- We streaked a single colony LB + Amp agar plate using K116002 glycerol stock. We incubated the plate at 37°C overnight.
- Preparation of LBK (LB with potassium instead of sodium) at pH 5,5 - 6,6 - 7,5 - 8,5 for the first experiment we would have performed in the following days.
September, 2nd
- Miniprep for:
- B5new2-3
- B6-3
- A11-3
- A4
- F2620MIT1
- E0240 pellet (stored at -20°C)
- Digestions:
- B5new2-3(E-X)
- B6-3(E-X)
- A11-3(S-P)
- A4(E-S)
- F2620MIT1(E-S)
- E0240(X-P)
- Gel run, cut and band purification for all the samples.
- Ligations:
- B7new = A4(E-S) + B5new2-3(E-X) in pSB1AK3
- B8new = A4(E-S) + B6-3(E-X) in pSB1AK3
- B9 = F2620MIT1(E-S) + B5new2-3(E-X) in pSB1AK3
- B10 = F2620MIT1(E-S) + B6-3(E-X) in pSB1AK3
- A14L = A11-3(S-P) + E0240(X-P) in pSB1A2
- We incubated the five reactions at 16°C overnight.
- Transformation/plating for A17new ligation.
- We inoculated a single colony from K116002 streaked plate in 5 ml of LB + Amp. We incubated the inoculum at 37°C, 220 rpm overnight.
pH sensor
- The plate showed grown colonies, we picked one colony and infected 1 ml of LB + Amp.
- Overnight incubation.
September, 3rd
- Miniprep for K116002 overnight culture. We used 1 ul of this sample to transform TOP10 in order to have the pH sensor in the same strain as the reference promoter (i.e. A2). We incubated the plate (LB + Amp) with transformed bacteria overnight at 37°C. We also sent purified DNA to BMR Genomics for sequencing.
- A17new overnight plate showed only one colony...easy screening for this plate! Colony PCR/electrophoresis for this sample. We stored this colony in 100ul of LB + Amp and incubated it at 37°C waiting for the end of the reaction.
- Gel results: the blank was not so clean, but the only colony was positive:) We inoculated the colony in 5 ml of LB + Amp to grow an overnight culture (37°C, 220 rpm).
- We transformed these ligations:
- B7new 1:40 on Kan
- B8new 1:40 on Kan
- B9 1:40 on Kan
- B10 1:40 on Kan
- A14L 1:20 on Amp
- We incubated B7new, B8new, B9 and B10 at 37°C in the morning. Then, five colonies for each plate were picked after about 11 hours. We inoculated these colonies in 5 ml of LB + Kan and incubated them overnight (37°C, 220 rpm). NOTE: B7new and B8new had smaller colonies than B9 and B10.
- We incubated A14L plate overnight at 37°C.
pH sensor
- Miniprep for the culture.
- Transformation into TOP10 E.coli.
- We plated transformed bacteria and incubated overnight at 37°C.
September, 4th
- A14L plate showed colonies and K116002(TOP10) plate showed a bacterial carpet (with some single colony).
- We inoculated a single colony from K116002(TOP10) plate in 1 ml of LB + Amp and incubated this inoculum for about 6 hours (37°C, 220 rpm). Then, a glycerol stock was prepared.
- Colony PCR/electrophoresis for 6 colonies from A14L plate. Colonies were saved inoculating them in 1 ml of LB + Amp and incubating them at 37°C, 220 rpm waiting for the end of the reaction.
- Gel results: all the colonies showed the amplicon with the right size, but even some extra band...we decided to keep A14L-1 to stock all the colonies in glycerol. We also decided to keep A14L-1: we inoculated it in 5 ml of LB + Amp to grow an overnight culture to check the sequence.
- We received sequencing results for B8-5again(VF2) and it was not correct.
- Glycerol stock/miniprep for 21 cultures:
- B7new X5 colonies
- B8new X5 colonies
- B9 X5 colonies
- B10 X5 colonies
- A17new
- We sent A17new purified DNA to BMR Genomics for sequencing.
- Screening (E-P digestion cut) for B7new, B8new, B9 and B10 samples.
pH sensor
The plate showed grown colonies.
- We picked a single colony and infected 4 ml LB + Amp.
- Incubation overnight.
September, 5th
pH sensor
- Glycerol stock for the overnight TOP10 E.coli culture containing pNhaA + GFP + Amp plasmid.
September, 6th
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