Team:Caltech/Notebook/Coliroid

From 2012.igem.org

(Difference between revisions)
 
(7 intermediate revisions not shown)
Line 1: Line 1:
{{Template:Caltech_Header}}
{{Template:Caltech_Header}}
-
{{Template:Caltech_Coliroid_Notebook}}
+
<html>
-
{|
+
<h1>Bacterial Animation Notebook</h1>
-
|-valign="top" border="0"
+
-
|width="1000px" style="padding: 0 20px 0 0;"|
+
-
 
+
-
 
+
-
==='''Coliroid Notebook'''===
+
-
 
+
-
<html>
+
<font size="+2"><a name="6_22_12">6/22/12</a></font>
<font size="+2"><a name="6_22_12">6/22/12</a></font>
Line 301: Line 294:
<p>
<p>
Miniprep M30109 and send off for sequencing. Order lacZ primers. Double check mCherry constructs. Add terminator to E1010 + R0082 constructs.   
Miniprep M30109 and send off for sequencing. Order lacZ primers. Double check mCherry constructs. Add terminator to E1010 + R0082 constructs.   
 +
Daisy - plated pSB1AC3 on LB+carb and LB+chlor plates; started an overnight culture of E. coli containing pSB1AC3
 +
</p>
 +
<br>
 +
<a a style="float:right;" href="https://2012.igem.org/Team:Caltech/Notebook/Coliroid#Calendar">Back to Coliroid Notebook Calendar</a>
 +
<br>
 +
<br>
 +
 +
<font size="+2"><a name="8_18_12">8/18/12</a></font>
 +
<br>
 +
<p> 
 +
Daisy - miniprepped pSSB1AC3
</p>
</p>
<br>
<br>
Line 361: Line 365:
<p>
<p>
Send R0040+mCherry-LVA/AAV for sequencing.  
Send R0040+mCherry-LVA/AAV for sequencing.  
 +
</p>
 +
<br>
 +
<a a style="float:right;" href="https://2012.igem.org/Team:Caltech/Notebook/Coliroid#Calendar">Back to Coliroid Notebook Calendar</a>
 +
<br>
 +
<br>
 +
 +
<font size="+2"><a name="9_11_12">9/11/12</a></font>
 +
<br>
 +
<p>
 +
There are some small colonies for pSB1C3 and mCherry-LVA/AAV! Redoing PCR of cph8 and mCherry untagged.
 +
</p>
 +
<br>
 +
<a a style="float:right;" href="https://2012.igem.org/Team:Caltech/Notebook/Coliroid#Calendar">Back to Coliroid Notebook Calendar</a>
 +
<br>
 +
<br>
 +
 +
<font size="+2"><a name="9_12_12">9/12/12</a></font>
 +
<br>
 +
<p>
 +
Redid PCR of mcherry untagged + cph8 usingi individual primers, not a primer mix. Gel showed that mCherry untagged PCR is successful.
 +
</p>
 +
<br>
 +
<a a style="float:right;" href="https://2012.igem.org/Team:Caltech/Notebook/Coliroid#Calendar">Back to Coliroid Notebook Calendar</a>
 +
<br>
 +
<br>
 +
 +
<font size="+2"><a name="9_13_12">9/13/12</a></font>
 +
<br>
 +
<p>
 +
Redo PCR for cph8 using 65C as annealing temperature and increasing the time for extension.Gel shows that cph8 PCR is successful! PCR clean up mcherry untagged + cph8. Digested mcherry with E & S and X & P and cph8 with X & P. PCR clean up again after digestion and ligate cph8 + R0040, cph8 + pSB1C3 (X & P), mcherry + pSB1C3 (X & P), and mcherry + pSB1C3 (E & S). Transformed and made overnights of RU1012 and JT2 coliroid strains.
 +
</p>
 +
<br>
 +
<a a style="float:right;" href="https://2012.igem.org/Team:Caltech/Notebook/Coliroid#Calendar">Back to Coliroid Notebook Calendar</a>
 +
<br>
 +
<br>
 +
 +
<font size="+2"><a name="9_14_12">9/14/12</a></font>
 +
<br>
 +
<p>
 +
The cph8 + R0040 carb plate had colonies. Did colony PCR and gel showed that ____. The three pSB1C3 plates had no colonies as they were plated on chlor + RM + amp, instead of just LB + chlor. Made chlor plates today. Made competent cells out of RU1012 and JT2 overnights. Transformed PCB and M30109 into RU1012 and JT2 (for a total of 4 transformations).
 +
</p>
 +
<br>
 +
<a a style="float:right;" href="https://2012.igem.org/Team:Caltech/Notebook/Coliroid#Calendar">Back to Coliroid Notebook Calendar</a>
 +
<br>
 +
<br>
 +
 +
<font size="+2"><a name="9_17_12">9/17/12</a></font>
 +
<br>
 +
<p>
 +
Out of the 7 transformations, the M30109 + JT2 and the M30109 + RU1012 plate had colonies. Made overnights of them and PL-PCB, pSB1C3, and R0040.
 +
</p>
 +
<br>
 +
<a a style="float:right;" href="https://2012.igem.org/Team:Caltech/Notebook/Coliroid#Calendar">Back to Coliroid Notebook Calendar</a>
 +
<br>
 +
<br>
 +
 +
<font size="+2"><a name="9_18_12">9/18/12</a></font>
 +
<br>
 +
<p>
 +
Miniprepped all the overnights. PCR of pvH001 with four new primers to make mcherry untagged, mcherry-LVA, and mcherry-AAV. Ran a gel and PCR clean up and elute with 50 ul EB. Digest for 1 hour at 37C. Digest all the mcherry's with E&S and X&P. For the mcherry digest with X&P, add Dpn1. Digest R0040 with S&P and pSB1C3 with E&S and X&P. Then agg 1 ul of CIP enzyme to pSB1C3 (X&P) and incubate at 37C for 1 hour. PCR cleanup and elute with 30 ul of EB and nanodrop. Then ligate the three mcherry's like mcherry-untagged/LVA/AAV + pSB1C3 (E&S), mcherry-untagged/LVA/AAV + pSB1C3 (X&P), and mcherry-untagged/LVA/AAV (X&P) + R0040 (E&S)
 +
Then run a gel and transform! 
</p>
</p>
<br>
<br>

Latest revision as of 01:06, 4 October 2012



Bacterial Animation Notebook

6/22/12

Transformed M30109 and R0082, M30109 had 3 colonies and R0082 had none.


Back to Coliroid Notebook Calendar
6/25/12

Re-transformed R0082, but with no colonies.


Back to Coliroid Notebook Calendar
6/26/12

Ran PCR of R0082 with OneTaq polymerase, gel had no band.


Back to Coliroid Notebook Calendar
6/27/12

PCR R0082 with vf2 and vr primers and Phusion polymerase. Gel had confirmed band length. PCR purified and had 34.6 ng/ul.


Back to Coliroid Notebook Calendar
6/28/12

Both R0082 and positive control plates had colonies. Transformed RFP (E1010) and lacZ and plated.


Back to Coliroid Notebook Calendar
6/29/12

PCR lacZ and pVH001 (mCherry-AAV Victoria's construct) and ran gel with correct band length for lacZ. There is lacZ DNA, but past lacZ transformations have not worked. Miniprepped overnight cultures of R0082 (43.6 ng/ul) and M30109 (28.9 ng/ul).


Back to Coliroid Notebook Calendar
7/2/12

Transformed lacZ again and sent R0082 and M30109 for sequencing. Started overnights of R0082, E1010, and MG1655.


Back to Coliroid Notebook Calendar
7/3/12

We transformed pSBC13 into Mg1655 on 3 different plates. We put 1 microliter of Mg1655 on 1 plate, 10 microliters on the second plate, and 100 microliters on the third plate, in order to figure out which one would make the best looking plate of red E. coli. We also miniprepped samples of R0028 and E1010.


Back to Coliroid Notebook Calendar
7/5/12
We double digested R0082, lacZ, and E1010 (RFP). We ran the digested samples on a gel along with undigested samples of each to make sure the digests worked. The lacZ and the E1010 digests were successful, but the gel results on the R0082 were inconclusive. We also transformed pSBC13 into Mg1655, but the LB was contaminated so we did not plate the culture.
Back to Coliroid Notebook Calendar
7/6/12

We started another culture for M1655 since our previous culture was made with contaminated LB. Then we re-digested the R0082 and ran a gel comparing the digested R0082 with the undigested. The digest was successful, so tested the concentrations of DNA in the R0082, the E1010, and the lacZ samples with the Nanodrop. There was not a high enough concentration of the E1010 DNA, so we could not use it in ligation. We ligated the R0082 with the E1010 and plated the plasmid. Also, we ordered primers for mCherry-AAV, mCherry-LVA, and mCherry.
Back to Coliroid Notebook Calendar
7/9/12

We found that there was growth on the ligation plate and no growth on the negative control plate, which was good. We checked to make sure that the ligation of R0082 and E1010 worked by running a PCR of 6 different colonies on the ligation plate as well as a sample of the undigested R0082 and then running a gel of these things.


Back to Coliroid Notebook Calendar
7/10/12

Started 5 cultures of ligated colony of RFP and R0082 to shake for 5-6 hours and then streak out on plates. Ran gel of lacZ PCR product.


Back to Coliroid Notebook Calendar
7/11/12

Ran gel to check lacZ digest, and PCR purified. PCR mCherry-AAV/LVA and streaked plate of M30109.


Back to Coliroid Notebook Calendar
7/12/12

Ran gel for mCherry, PCR purified mCherry, M30109 had no colonies. Started overnights for R0082.


Back to Coliroid Notebook Calendar
7/13/12

To do: Digest mCherry and R0082, run gel to make sure. PCR purify, then ligate mCherry+R0082 and lacZ+R0082


Back to Coliroid Notebook Calendar
7/16/12

Ligated R0082 with lacZ, mCherry-LVA, mCherry-AAV and plated. Transformed another lacZ part (BBa_I732019).


Back to Coliroid Notebook Calendar
7/17/12

There was growth on the lacZ, mCherry-AAV, and mCherry-LVA ligation plates. We did a colony pcr and re-struck colonies for these plates as well as for the E1010-R0082 ligation plate.


Back to Coliroid Notebook Calendar
7/18/12

We ran a gel on the colony pcrs of the lacZ, mCherry-AAV, mCherry-LVA, and E1010 ligation plates. The gel showed that the ligations had apparently not worked, so we re-digested the mCherries and the R0082 to start over the process of ligation.


Back to Coliroid Notebook Calendar
7/19/12

We ran a gel on the digests of the mCherries and R0082, and it appeared to have worked, so we ligated mCherry-AAV + R0082 and mCherry-LVA + R0082, then ran a gel.


Back to Coliroid Notebook Calendar
7/20/12

We re-did a ligation on the mCherries and R0082 because it appeared from the gel that the ligation from Friday did not work.


Back to Coliroid Notebook Calendar
7/23/12

Ran a gel of re-ligated R0082 and mCherry-LVA,mCherry-AAV.


Back to Coliroid Notebook Calendar
7/24/12

Plated the mCherry ligations 2, 3, and negative control.


Back to Coliroid Notebook Calendar
7/24/12

The four mCherry ligations plates have colonies and the negative control plate has some, but not many compared to the ligated colonies. Colony PCR on the ligations and negative control. PCR mCherry-LVA and mCherry-AAV with dpn1 digest? Make plates with agar embedded.


Back to Coliroid Notebook Calendar
7/25/12

Ran a gel and imaged the ligations and confirmed the ligations worked. Overnights of ligation for miniprep for tomorrow morning.


Back to Coliroid Notebook Calendar
7/26/12

Started overnight cultures of mCherry ligations with varying salt concentrations (0, 0.25, 0.5, .75, 1 mol NaCl) and one growing in water. Sent mCherry ligations off for sequencing.


Back to Coliroid Notebook Calendar
7/27/12

Overnight cultures have no apparent redness, looked at cultures with plate reader for any RFP, but there is very little which may be background. The RFP created may have been degraded by the degradation tags.


Back to Coliroid Notebook Calendar
7/30/12

Amplify lacZ out of E. coli genome.


Back to Coliroid Notebook Calendar
8/3/12

Transformed and plated multiple parts: cph8, cph8 + PCB (missing terminator), PCB from Lagarias, cph1 from Lagarias.


Back to Coliroid Notebook Calendar
8/3/12

Every plate has many colonies, too many colonies.


Back to Coliroid Notebook Calendar
8/3/12

The plates in the fridge were contaminated, and my plates had some contamination, so I need to throw them out and transform again! Made new batch of Carb-Amp, Chlor, and Kan plates.


Back to Coliroid Notebook Calendar
8/3/12

Re-transformed all plates: K321224, K321227, PL-PCB, PTYB2-cph1, I12013.


Back to Coliroid Notebook Calendar
8/16/12

PL-PCB, PTYB2-cph1, and I12013 had colonies. Restreak them out to isolate a colony and restreak M30109 from Agar Stab from parts registry.


Back to Coliroid Notebook Calendar 8/17/12

Miniprep M30109 and send off for sequencing. Order lacZ primers. Double check mCherry constructs. Add terminator to E1010 + R0082 constructs. Daisy - plated pSB1AC3 on LB+carb and LB+chlor plates; started an overnight culture of E. coli containing pSB1AC3


Back to Coliroid Notebook Calendar

8/18/12

Daisy - miniprepped pSSB1AC3


Back to Coliroid Notebook Calendar

9/4/12

Transform R0040 (tetR promoter).


Back to Coliroid Notebook Calendar

9/5/12

PCR mCherry-LVA/AAV. Digest with E & S and ligate to E & S digested pSBC13. Transform mCherry-LVA/AAV, M30109, PCB. Make overnights of R0040. Order primers for regular mCherry construct. Order primers to PCR out cph8 from M30109 and for regular mCherry PCR.


Back to Coliroid Notebook Calendar

9/6/12

Miniprep R0040 and send for sequencing. Digest, ligate and transform R0040 with mCherry-LVA/AAV.


Back to Coliroid Notebook Calendar

9/7/12

Make overnights of R0040 + mCherry-LVA/AAV.


Back to Coliroid Notebook Calendar

9/8/12

Miniprep R0040+mCherry-LVA/AAV.


Back to Coliroid Notebook Calendar

9/10/12

Send R0040+mCherry-LVA/AAV for sequencing.


Back to Coliroid Notebook Calendar

9/11/12

There are some small colonies for pSB1C3 and mCherry-LVA/AAV! Redoing PCR of cph8 and mCherry untagged.


Back to Coliroid Notebook Calendar

9/12/12

Redid PCR of mcherry untagged + cph8 usingi individual primers, not a primer mix. Gel showed that mCherry untagged PCR is successful.


Back to Coliroid Notebook Calendar

9/13/12

Redo PCR for cph8 using 65C as annealing temperature and increasing the time for extension.Gel shows that cph8 PCR is successful! PCR clean up mcherry untagged + cph8. Digested mcherry with E & S and X & P and cph8 with X & P. PCR clean up again after digestion and ligate cph8 + R0040, cph8 + pSB1C3 (X & P), mcherry + pSB1C3 (X & P), and mcherry + pSB1C3 (E & S). Transformed and made overnights of RU1012 and JT2 coliroid strains.


Back to Coliroid Notebook Calendar

9/14/12

The cph8 + R0040 carb plate had colonies. Did colony PCR and gel showed that ____. The three pSB1C3 plates had no colonies as they were plated on chlor + RM + amp, instead of just LB + chlor. Made chlor plates today. Made competent cells out of RU1012 and JT2 overnights. Transformed PCB and M30109 into RU1012 and JT2 (for a total of 4 transformations).


Back to Coliroid Notebook Calendar

9/17/12

Out of the 7 transformations, the M30109 + JT2 and the M30109 + RU1012 plate had colonies. Made overnights of them and PL-PCB, pSB1C3, and R0040.


Back to Coliroid Notebook Calendar

9/18/12

Miniprepped all the overnights. PCR of pvH001 with four new primers to make mcherry untagged, mcherry-LVA, and mcherry-AAV. Ran a gel and PCR clean up and elute with 50 ul EB. Digest for 1 hour at 37C. Digest all the mcherry's with E&S and X&P. For the mcherry digest with X&P, add Dpn1. Digest R0040 with S&P and pSB1C3 with E&S and X&P. Then agg 1 ul of CIP enzyme to pSB1C3 (X&P) and incubate at 37C for 1 hour. PCR cleanup and elute with 30 ul of EB and nanodrop. Then ligate the three mcherry's like mcherry-untagged/LVA/AAV + pSB1C3 (E&S), mcherry-untagged/LVA/AAV + pSB1C3 (X&P), and mcherry-untagged/LVA/AAV (X&P) + R0040 (E&S) Then run a gel and transform!


Back to Coliroid Notebook Calendar

Retrieved from "http://2012.igem.org/Team:Caltech/Notebook/Coliroid"