Team:University of Lethbridge/Notebook/GeneralLabAugust

From 2008.igem.org

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(Aug. 1- 7 belong in other August notebooks)
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[[Team:University_of_Lethbridge/Notebook|Back to The University of Lethbridge Main Notebook]]
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===August 1, 2008===
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====Nathan Puhl, Roxanne====
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Riboswitch 20 uL PCR. Set up 4 reactions (25 uL for each total volume). 1 uL or 1/100 pTopp and 1 uL or H1/100 PCR from July 28, 2008.
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PCR conditions:
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A. Initial denaturation: 98 C (3 min)
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B. -Denaturation: 98 C (10 sec)
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    - Annealing: 55 C (30 sec)
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    -Extension: 72 C (15 sec)
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    -30 cycles
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C. Final extension: 72 C (7 min)
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===August 2, 2008===
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====Nathan Puhl, Roxanne====
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Ran riboswitch (Aug. 1, 2008) on 3% agarose gel. Results are in the hard copy lab notebook. Looks like 76 bp band will extract.
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===August 5, 2008===
===August 5, 2008===
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===August 6, 2008===
===August 6, 2008===
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====Nathan Puhl et al====
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====Nathan Puhl, Roxanne====
2 color reporter system:
2 color reporter system:
Gel extracted LacI insert and DT vector. Didn't run gel yet.
Gel extracted LacI insert and DT vector. Didn't run gel yet.
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===August 7, 2008===
 
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====Nathan Puhl, Roxanne====
 
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Riboswitch:
 
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-
Set up PCR using purified riboswitch from Aug. 5, 2008 with platinum Taq (50 uL reaction). Made Master Mix for three reactions.
 
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Master Mix:
 
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-10x Buffer (no Mg2+): 15 uL
 
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-10 mM dNTPs: 3 uL
 
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-50 mM Mg2+: 4.5 uL
 
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-10uM RF: 3 uL
 
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-10uM RR: 3 uL
 
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-Plat. poly: 0.6 iL
 
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-H20: 120.9 uL
 
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-template: 1 uL
 
-
 
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Cycle conditions:
 
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A. Initial denaturation: 94 C (2 min)
 
-
B. -Denaturation: 94 C (30 sec)
 
-
    - Annealing: 55 C (30 sec)
 
-
    -Extension: 72 C (30 sec)
 
-
    -30 cycles
 
-
C. Final extension: 72 C (7 min)
 
===August 13, 2008===
===August 13, 2008===
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===August 16, 2008===
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===August 15, 2008===
====Roxanne====
====Roxanne====
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Ran Plasmids in a 1% Agarose Gel at 100 V for 30 minutes.
Ran Plasmids in a 1% Agarose Gel at 100 V for 30 minutes.
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===August 18===
 
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====Christa, Nathan Puhl, Munima====
 
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Ran a colony PCR of riboswitch extracted from gel done by Nathan and Roxanne on a previous day.  Roxanne will remove the PCR tube from the thermocycler in the morning.
 
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===August 19, 2008===
 
-
 
-
====Roxanne====
 
-
-Ran the PCR Product on a 1% Agarose Gel.
 
====Christa, Munima, Sebastian====
====Christa, Munima, Sebastian====
Line 116: Line 66:
Conclusion: The bands appeared to be at the correct size for pSB1A7.
Conclusion: The bands appeared to be at the correct size for pSB1A7.
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===August 22, 2008===
===August 22, 2008===
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Objective: Run a gel to confirm that appropriate inserts were amplified from the PCRs and do a gel extraction of the inserts to prepare them for the biobrick format.
Objective: Run a gel to confirm that appropriate inserts were amplified from the PCRs and do a gel extraction of the inserts to prepare them for the biobrick format.
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  -Could not obtain a picture of the gel (1% agarose) of the digested pSB1A7 and the recently amplified CheZ gene (15 uL x 3 wells) because the camera would not turn on.  
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  -Could not obtain a picture of the gel (1% agarose) of the half of the digested pSB1A7 (15 uL x 3 wells) and  
 +
the recently amplified  
 +
CheZ gene (15 uL x 3 wells) because the camera would not turn on.  
   The CheZ gene appeared at the correct size (~700 bp).
   The CheZ gene appeared at the correct size (~700 bp).
-
  -Did a gel extraction of pSB1A7 and CheZ from that gel with the Qiagen MiniElute Gel Extraction kit. Final volume of each was 10 uL.
+
  -Did a gel extraction of pSB1A7 and CheZ from that gel with the Qiagen MiniElute Gel Extraction kit.  
-
  -Ran another 1% agarose gel to confirm that the gel extraction was successful. Ran 1 uL of each sample. Bands appeared at appropriate sizes. The concentrations of pSB1A7  
+
Final volume of each was 10 uL.
 +
  -Ran another 1% agarose gel to confirm that the gel extraction was successful. Ran 1 uL of each sample.  
 +
Bands appeared at appropriate sizes. The concentrations of pSB1A7  
   and CheZ were estimated to be 25 ng/uL and 80 ng/uL, respectively.
   and CheZ were estimated to be 25 ng/uL and 80 ng/uL, respectively.
-
Next step: Digest both pSB1A7 and CheZ with phosphatase. A restriction digest will be performed at a later date on CheZ to prepare it for insertion.
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Next step: Digest pSB1A7 with antarctic phosphatase. A restriction digest will be performed at a later date on CheZ to prepare it for insertion.
 +
 
 +
 
 +
===August 26, 2008===
 +
====Roxanne, John====
 +
-Restriction Digested the Biobrick Parts I13504, I13401, P0440, C0014, B0015, J31007 with XbaI and PstI
 +
 
 +
-20 uL template (~2 ug)
 +
-5 uL React 2
 +
-4 uL XbaI
 +
-4 uL PstI
 +
-17 uL ddH2O
 +
____
 +
50uL Reaction in 37.0C H2O bath overnight
 +
 
 +
 
 +
===August 27, 2008===
 +
====Roxanne====
 +
-Inactivated the Restriction Enzymes by placing them on the heating block at 65.0C for 10 minutes
 +
-Ran 25uL of DNA on a 1% Agarose Gel at 100 V for 30 minutes
 +
-Gel Extracted the DNA
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-Ran 1 uL of DNA in a 1% Agarose Gel at 100V for 30 minutes.
 +
 
 +
[[Image:Biobrick_Parts.jpg| 250 px]]
 +
 
 +
 
 +
===August 28, 2008===
 +
====Roxanne, Munima, Sebastian, Nathan Puhl====
 +
-Performed a restriction digest on LacI+dt, pLacI, pStrong, and RFP sub
 +
 
 +
-10 uL template
 +
-5 uL NEB 2
 +
-2 uL Restriction Enzyme #1 (Xba I or Spe I)
 +
-2 uL Restriction Enzyme #2 (Pst I)
 +
-21 uL ddH20
 +
____
 +
50 uL Rxn left to run overnight at 37.0
 +
 
 +
-Ran a Gel of the Riboswitch PCR which had been done with Taq a couple of weeks ago to quantify the amount of DNA present. Setup the Math to perform a ligation into pGEM T-easy.
 +
 
 +
-Picked a colony from the dT plate which was stored in the fridge from several weeks ago, incubated overnight at 37.0C
 +
 
 +
 
 +
===August 29, 2008===
 +
====Roxanne, Nathan Puhl, Munima, Sebastian, Andrew====
 +
-Performed the ligation of the riboswitch into pGEM T-easy, transformed and plated.
 +
 
 +
=====Roxanne====
 +
-Gel Extracted the remainder of the DNA
 +
 
 +
 
 +
===August 30, 2008===
 +
====Nathan Puhl, Roxanne, Andrew====
 +
-Ran a gel of the Digested Parts on 1% Agarose @ 100V for 27 minutes.

Latest revision as of 02:29, 30 October 2008

Back to The University of Lethbridge Main Notebook

Contents

August 5, 2008

Nathan Puhl et al

Gel extracted two bands really closer to each other from PCR (August 1) at ~76 bp. Used Qiagen MiniElute kit. Results are in the hard copy lab notebook. Seems as if gel extraction was successful. ____ 2 color reporter system:

Set up digest of LacI and DT.

LacI - EcoRI and SpeI

DT - EcoRI and XbaI

Reaction mixture: 

-5 uL template
-5 uL NEB 2 Buffer
-0.5 uL BSA?
-1 uL RE #1
-1 uL RE #2
- 37.5 uL ddH20

Left at 37 C overnight. Heat deactivation (65 C) for 15 minutes.


August 6, 2008

Nathan Puhl, Roxanne

2 color reporter system:

Gel extracted LacI insert and DT vector. Didn't run gel yet.


August 13, 2008

Nathan Puhl and Sebastian

Verified and quantified the LacI and DT restriction digest products.

Set up a Ligase experiment for LacI and DT 

- 1.3 uL vector(DT)
- 8 uL insert(LacI)
- 2 uL 10x Ligase buffer
- 1.5 uL Ligase
- 7.2 uL ddH2O
- 20 uL total volume


August 14, 15

Nathan Puhl, Munima, Selina

Poured 61 LB + Amp plates. Stored in iGEM 4 C fridge.


August 15, 2008

Roxanne

Used Qiagen Plasmid MiniPrep Kit to Plasmid Prep Last Year's Biobrick Parts that were Incubated overnight.

Ran Plasmids in a 1% Agarose Gel at 100 V for 30 minutes.

Christa, Munima, Sebastian

Did a plasmid prep on pSB1A7 using QIAprep Spin Miniprep Kit. Stocked 4- 50uL of pSB1A7 and stored in iGEM -20 C.

Sebastian, Nathan Puhl

Ran products from plasmid prep (pSB1A7 x 4 samples) on 1% agarose gel for 27 minutes. 

-Lane 1 - 1 kb GeneRuler ladder (2 uL)
-Lane 2 -6 pSB1A7 (3 uL) + 6x loading dye (2 uL); Mixed up what sample was in Lane 4, so Lanes 5 and 6 were run.

Conclusion: The bands appeared to be at the correct size for pSB1A7.


August 22, 2008

Christa, Munima, Nathan Puhl, Roxanne

Objective: Run a gel to confirm that appropriate inserts were amplified from the PCRs and do a gel extraction of the inserts to prepare them for the biobrick format. 

-Could not obtain a picture of the gel (1% agarose) of the half of the digested pSB1A7 (15 uL x 3 wells) and 
the recently amplified 
CheZ gene (15 uL x 3 wells) because the camera would not turn on. 
  The CheZ gene appeared at the correct size (~700 bp).
-Did a gel extraction of pSB1A7 and CheZ from that gel with the Qiagen MiniElute Gel Extraction kit. 
Final volume of each was 10 uL.
-Ran another 1% agarose gel to confirm that the gel extraction was successful. Ran 1 uL of each sample. 
Bands appeared at appropriate sizes. The concentrations of pSB1A7 
  and CheZ were estimated to be 25 ng/uL and 80 ng/uL, respectively.

Next step: Digest pSB1A7 with antarctic phosphatase. A restriction digest will be performed at a later date on CheZ to prepare it for insertion.


August 26, 2008

Roxanne, John

-Restriction Digested the Biobrick Parts I13504, I13401, P0440, C0014, B0015, J31007 with XbaI and PstI 

-20 uL template (~2 ug)
-5 uL React 2
-4 uL XbaI
-4 uL PstI
-17 uL ddH2O
____
50uL Reaction in 37.0C H2O bath overnight


August 27, 2008

Roxanne

-Inactivated the Restriction Enzymes by placing them on the heating block at 65.0C for 10 minutes -Ran 25uL of DNA on a 1% Agarose Gel at 100 V for 30 minutes -Gel Extracted the DNA -Ran 1 uL of DNA in a 1% Agarose Gel at 100V for 30 minutes.

Biobrick Parts.jpg


August 28, 2008

Roxanne, Munima, Sebastian, Nathan Puhl

-Performed a restriction digest on LacI+dt, pLacI, pStrong, and RFP sub 

-10 uL template
-5 uL NEB 2
-2 uL Restriction Enzyme #1 (Xba I or Spe I)
-2 uL Restriction Enzyme #2 (Pst I)
-21 uL ddH20
____
50 uL Rxn left to run overnight at 37.0

-Ran a Gel of the Riboswitch PCR which had been done with Taq a couple of weeks ago to quantify the amount of DNA present. Setup the Math to perform a ligation into pGEM T-easy.

-Picked a colony from the dT plate which was stored in the fridge from several weeks ago, incubated overnight at 37.0C


August 29, 2008

Roxanne, Nathan Puhl, Munima, Sebastian, Andrew

-Performed the ligation of the riboswitch into pGEM T-easy, transformed and plated.

=Roxanne

-Gel Extracted the remainder of the DNA


August 30, 2008

Nathan Puhl, Roxanne, Andrew

-Ran a gel of the Digested Parts on 1% Agarose @ 100V for 27 minutes.

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