Lab Notebook

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== August 27, 2007 ==
 
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Start Time: 11:00 pm – End Time: 3:00 pm
 
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Members Present: Yusuf, Mimi, Talal
 
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• Carried out plasmid digest (length checks) on I 13507 B and J 37033 B
 
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• '''Length Check results:'''
 
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''I 13507 B – Overall 3 bands were seen for this plasmid''
 
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6-7 (Closer to 7 than to 6)
 
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8-9 (Closer to 9 than to 8)
 
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11-12 (Closer to 11 than to 12)
 
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The number of parts and parts and plasmid match up closely but the first band between 6-7 could be of the uncut plasmid
 
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''J 37033 B – Overall 2 bands were seen''
 
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8-9 (Closer to 9 than to 8)
 
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10-11 (In the middle)
 
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The bands formed doesn’t match up with the given numbers for its part and plasmid from the registry
 
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• Did Mini-prep overnight for F 1610  with 4 colonies labeled A', B', C', D' and put it in the incubator
 
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== August 23, 2007 ==
 
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Start time: 6:30pm
 
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F/T: Anam
 
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P/T: Fareeha
 
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-Done length check PD for all of A, green circle B, red circle B, black dot B
 
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-Enzymes X and P used for all except for J23100 because the part is too small and so the plasmid that contained it was linearized using enzyme P.
 
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-Buffer 2 was used.
 
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Results:
 
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-All were correct length except for samples from colonies A and B of F1610 and colony A of J37033.
 
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- S01003 (colony A), S01414 (colony B), I13507 (colony A) had 3 bands.
 
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- The 3rd band might have shown up because some of the plasmid was only cut in one location.
 
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To do list:
 
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1) Do a PD length check for the rest of the samples
 
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2) Discuss with Yusuf how much information needs to be recorded when observing the bands in a gel for PD length check
 
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Note: There is one gel left in the fridge. It was made today.
 
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== August 24, 2007 ==
 
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Time: 5 pm
 
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F/T: Anam
 
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P/T: Talal
 
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-Record the results of the gel Yusuf had made and run (included in table below)
 
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-PD length check for J23100 colony C successful.
 
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-1 band between 6 and 7 on gel
 
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== August 22, 2007 ==
 
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Start Time: 5:30 pm – End Time: 7:30 pm
 
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Members Present: Yusuf, Anam
 
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• We did Mini Prep overnight and since I did 7 transformations, we decided to do 4 copies of each labeled A,B,C,D so that we have more flexibility in choosing our parts properly.
 
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• These are the following symbols we used to clarify all the tubes with the parts
 
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Black circle - I 13507 (AMP Res) (A – D)
 
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Red circle - F 1610 (AMP & KAN Res) (A – D)
 
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Green Dot - S 01640 (AMP Res) (A – D)
 
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Black dot - S 01414 (AMP Res) (A – D)
 
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Red dot - J 37033 (AMP Res) (A – D)
 
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Black line - J 23100 which is a promoter (AMP Res) (A – D)
 
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Red line - S 01003 (AMP Res) (A – D)
 
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• We also labeled our colonies from the Agar plates which were chosen for miniprep overnight  as it was instructed by Seema to both Anam and Esther.
 
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• The cells which had the promoter J 23100 were light pink colored if Charles and Andy would like to shed some light upon that that would be great.
 
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== August 21, 2007 ==
 
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Start Time: 11:00 am
 
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• Charles showed me how to use the registry properly so if anyone needs to know  how to use the registry properly just let me know.
 
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o We searched for super parts which is more like a couple of parts ligated together so that it makes our job a lot easier
 
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o So we chose 7 parts to be transformed from the neural network MODIFIED model
 
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• Part timer Muhammad Talal Latif showed up and I instructed him on how to do transformation properly
 
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• So I used 20 l of TE buffer to extract:
 
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o J 37033: 8F, Plate:3 (Amp Res)
 
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o S 01640: 3L, Plate:3 (Amp Res)
 
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• Both of them were from the iGEM 2007 Kit Plates
 
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• We stored the plasmids in the –20C freezer labeled in red DNA remaining
 
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• Added 4 l  of J37033 and S01640 to separate competent cell (DH5Z1) eppendorf tubes from the –80C freezer
 
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• So now we are following the Transformation steps from the guidelines posted
 
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• We used two AMP plates made from before
 
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• We also made 8 AMP plates where 4 is going to be used today for the other four parts which we also transformed:
 
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o I 13507: (Used form 2005 stock) (AMP Res)
 
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o S 01003: 20O, Plate:1 (AMP Res)
 
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o J 23100: 21E, Plate: 3 (AMP Res)
 
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o S 01414: 22O, Plate: 1 (AMP Res)
 
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• We also made 3 AMP and KAN plates where 1 is going to be used:
 
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o F 1610: 1B, Plate: 2, (AMP and KAN Resistant)
 
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• CONFUSION: While making the AMP and KAN plates we used AMP of 100mg/ml whereas KAN was 30mg/ml. So even though KAN was of different concentration we used the same quantity.
 
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o CHARLES AND ANDY GIVE US SOME INSIGHT ON TO THIS TOPIC
 
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• So we left all 7 plates for overnight incubation and hopefully we see some results tomorrow
 
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• Everybody please welcome SeungMe (part time) who came in and helped me finish the work today and of course Charles
 

Latest revision as of 13:22, 30 August 2007