Difference between revisions of "Team:UChicago/Notebook"

·Made a list of things to order for the future
·Printed most of the protocols; they are located on the lab bench when needed
·Made LB, LB amp, and YED plates
·Note: LB amp plates did not turn out as well as the others; will reattempt on 6/13/2017
·LABELLING ON PLATES
·One red stripe → LB plate
·One red stripe with one blue stripe → LB Amp plate
·One black stripe → YED plates
·The plates have been left on the bench overnight; they will be put in the fridge tomorrow morning. Jason had cleared out a spot for us in the Glick fridge for our use!

·Redid the LB-amp plates
·Made the Drop-Out plates (-Arg)
·Talked to Shannon about cleaning our glassware
·Labelled our glassware
·The petri dishes are in the fridge (all made within the last two days)

·Learned how to use the Nanodrop
·Made two stocks of 500 mL LB media (1000 mL total)
·Testing optimal DNA concentrations for bacterial transformation:
·Spread six different DNA concentrations of the 126 ng/μl plasmid sample (AJ43) Jason gave us onto LB + amp plates
·Left these plates overnight in a 37℃ incubator
   ·Plate 1 = negative control (no DNA, contains 50 μl EB and 50 μl competent cells)
   ·Plate 2 = 453.6 ng DNA (3.6 μL DNA, 46.4 μL EB, 50 μL CC)
   ·Plate 3 = 315 ng DNA (2.5 μL DNA, 47.5 μL EB, 50 μL CC)
   ·Plate 4 = 239.4 ng DNA (1.9 μL DNA, 48.1 μL EB, 50 μL CC)
   ·Plate 5 = 201.6 ng DNA (1.6 μL DNA, 48.4 μL EB, 50 μL CC)
   ·Plate 6 = 163.8 ng DNA (1.3 μL DNA, 48.7 μL EB, 50 μL CC)
·Took a small sample of pOW1 (in frozen bacteria) from stock in the -80℃ fridge
·Put the pOW1 into 5 mL of LB + amp liquid media (1 μL ampicillin / 1 mL LB)
·Left the sample in the 37℃ shaker overnight to incubate

·Retrieved the AJ43 plates
·Negative control = no colonies
·1 = too many colonies to count
·2 = too many colonies to count
·pOW1 plating concentrations for next week:
   ·1 μL pOW1 + 49 μL EB + 50 μL CC
   ·2.5 μL pOW1 + 47.5 μL EB + 50 μL CC
   ·5 μL pOW1 + 45 μL EB + 50 μL CC

·Transformed the pOW1 DNA into competent cells
·Incubated the transformations for 2 hours in a 37℃ shaker
·Spread the samples on LB + amp plates
·Left the plates overnight in a 37℃incubator

-Observed the plates from the previous transformation
-Retrieved pOW1 plates

-Transformed the pOW1 DNA again into competent cells
1 = Negative control = 50 μL CC
2 = 0.5 μL pOW1 + 50 μL CC
3 = 10 μL pOW1 + 40 μL EB + 50 μL CC
4 = 15 μL pOW1 + 35 μL EB + 50 μL CC
5 = 20 μL pOW1 + 30 μL EB + 50 μL CC
-Cool website that gives you quick-change primers (by just entering the sequence you want to amplify):
QuikChange Primer Design
-Plated autotrophic (arg) yeast and non-autotrophic yeast on -Arg and +Arg
Incubated the two plates in 30℃ overnight
-PCR protocol for pSB1C3mut:

-Retrieved the yeast plates:

-Retrieved pOW1 plates:

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@@ Line 135: / Line 135: @@
 <div class="panel">
    <p>
--Task List:<br>
+&#183;Retrieved the AJ43 plates<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;-Mini-prep the pOW1 <br>
+&nbsp;  &nbsp;  &nbsp;  &nbsp;&#183;Negative control = no colonies<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;-Transform the isolated pOW1 DNA into competent cells<br>
+&nbsp;  &nbsp;  &nbsp;  &nbsp;&#183;1 = too many colonies to count<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;-Spread the competent cells on LB + amp plates<br>
+&nbsp;  &nbsp;  &nbsp;  &nbsp;&#183;2 = too many colonies to count<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;-Leave these plates overnight in a 37&#8451; incubator<br>
+&nbsp;  &nbsp;  &nbsp;  &nbsp;&#183;pOW1 plating concentrations for next week:<br>
--Retrieved the AJ43 plates<br>
+&nbsp;  &nbsp;  &nbsp;  &nbsp;&nbsp;  &nbsp;  &nbsp;  &nbsp;&#183;1 μL pOW1 + 49 μL EB + 50 μL CC<br>
+&nbsp;  &nbsp;  &nbsp;  &nbsp;&nbsp;  &nbsp;  &nbsp;  &nbsp;&#183;2.5 μL pOW1 + 47.5 μL EB + 50 μL CC<br>
+&nbsp;  &nbsp;  &nbsp;  &nbsp;&nbsp;  &nbsp;  &nbsp;  &nbsp;&#183;5 μL pOW1 + 45 μL EB + 50 μL CC<br>
-<div class="banner">
-    <div class="inline-block">
-                <figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" >
-<figcaption>Plate 1 = no colonies</figcaption>
-</figure>
-    </div>
-    <div class="inline-block">
-                <figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" >
-<figcaption>Plate 2 = too many to count</figcaption>
-</figure>
-    </div>
-    <div class="inline-block">
-        <figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250">
-<figcaption>Plate 3 = too many to count</figcaption>
-</figure>
-    </div>
-</div>
-<div style="display: flex; margin-top: 40px;margin-bottom: 35px; ">
- <figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" style="margin-right:100px;" >
-<figcaption>Plate 4 = more than 200 colonies</figcaption>
-</figure>
- <figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" style="margin-right:100px;" >
-<figcaption>Plate 5 = 53 colonies (the best plate we<br> got)</figcaption>
-</figure>
-<figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" style="margin-right:100px;" >
-<figcaption>Plate 6 = 3 colonies</figcaption>
-</figure>
-</div>
--Mini-prepped the pOW1 that had been incubating in the shaker overnight.<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;The best sample we got was 61.6 ng/μL DNA<br>
--Transformed the DNA into competent cells<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;Negative control = 50 μL CC<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;1 = 1 μL pOW1 sample, 50 μL CC<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;2 = 5 μL pOW1 sample, 50 μL CC<br>
--Incubated the transformations for 2 hours in a 37&#8451; shaker<br>
--Autoclaved pipette tips<br><br>
--Retrieved the pOW1 plates<br>
-<div style="display: flex; margin-top: 20px; margin-bottom: 35px; ">
-  <figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" style="margin-right:100px;" >
-<figcaption>Negative control = no colonies</figcaption>
-</figure>
- <figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" style="margin-right:100px;" >
-<figcaption>1 = too many colonies to count</figcaption>
-</figure>
-<figure><img src="https://static.igem.org/mediawiki/2017/9/97/T--UChicago--MTT.jpg" alt="Plate" width="250" height="250" style="margin-right:100px;" >
-<figcaption>2 = too many colonies to count</figcaption>
-</figure>
-</div>
--pOW1 plating concentrations for next week:<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;1 μL pOW1 + 49 μL EB + 50 μL CC<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;2.5 μL pOW1 + 47.5 μL EB + 50 μL CC<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;5 μL pOW1 + 45 μL EB + 50 μL CC<br>
 </p>
 </div>
@@ Line 210: / Line 150: @@
 <div class="panel">
    <p>
--Primers either to arrive on Tuesday or Wednesday<br>
+&#183;Transformed the pOW1 DNA into competent cells<br>
--Transformed the pOW1 DNA into competent cells<br>
+&#183;Incubated the transformations for 2 hours in a 37&#8451; shaker<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;1 = Negative control = 50 μL CC<br>
+&#183;Spread the samples on LB + amp plates<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;2 = 1 μL pOW1 + 49 μL EB + 50 μL CC<br>
+&#183;Left the plates overnight in a 37&#8451;incubator<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;3 = 2.5 μL pOW1 + 47.5 μL EB + 50 μL CC<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;4 = 5 μL pOW1 + 45 μL EB + 50 μL CC<br>
--Incubated the transformations for 2 hours in a 37&#8451; shaker<br>
--Spread the samples on LB + amp plates<br>
--Left the plates overnight in a 37&#8451;incubator<br>
--Tasks for tomorrow:<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;-Check on the plates<br>
-&nbsp;  &nbsp;  &nbsp;  &nbsp;-If the primers have arrived, start Workflow 1!<br>
 </p>
 </div>