Team:SDU-Denmark/labwork/Notebook/week3

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<h2>Laboratory Notebook</h2>
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<h1>Laboratory Notebook</h1>
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Here you find the log book for the procedures carried out in the laboratory, starting from week 27. 
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     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week8">8th week      </a></span>    </regulartext></td>
     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week8">8th week      </a></span>    </regulartext></td>
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week9">9th week</a></span>    </regulartext></td>
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                                            <!----------3rd WEEK---------->
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week10">10th week</a></span>    </regulartext></td>
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week11">11th week</a></span>    </regulartext></td>
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<p> <b>19-07-2012:</b> </p>
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<h2>Another digestion, plated SST cultures and Miniprep on FFT </h2> <br/>
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week12">12th week</a></span>     </regulartext></td>
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The plated SST from yesterday didn’t give any colonies. We tried a different procedure where we use the PCR purification from SST and the pJET plasmid digested with EcoRV in a gel. </br>
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</table>
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We then made a gel purification on both bands at the same time. </br>
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The purification was eluted in 30μl elution buffer, and then we used 7μl of the elution with 0,5μl ligase and 2,5μl ligase buffer in order to ligate the gene into the vector.
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This was plated on amp-agar plates and incubated O.N. </br>
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</br>
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We also made <a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/Miniprep">Miniprep</a> on the 10 liquid colonies with FFT, then digested it with EcoRI and PstI. </br>
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The digest was ran on a gel and proved results from FFT coloni 3 and 9 which had two bands corrosponding to our vector and gene. </br>
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We measured the concentration on the two tubes using the nano-dropper  and got the following concentrations: </br>
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<b>Tube#3:</b> 138,2ng/µl </br>
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<b>Tube#9:</b> 71,8ng/µl </br>
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This was enough reason to send them off for sequencing.  </br>
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Seeing as we needed to send of four tubes per sample with 15µl per tube, we didn’t have enough volume in tube#9, so we only prepared four tubes to be send off for sequencing of tube#3, as it had a slightly higher concentration than the 100ng/µL maximum, so we just added another 20µl of elution buffer for a total volume of 67µL in tube #3, which was then split into four tubes of 15µL and labelled with barcodes.
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</br>
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Furthermore we made 8 new coloni PCR’s  from the original FFT amp. agar plate.
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But we only got very small parts shown on the gel so it wasn't a success. </br>
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For the sequencing, we need four primers, a pJET1.2_for and _rev and then 2 primers that would anneal on the FFT gene. We used the MWG sites primer design tool (http://www.eurofinsdna.com/)  to design primers that anneal to the FFT gene. </br>
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Seeing as the FFT gene is approximately 1800bp long the primers were designed to anneal somewhere between positions 450-500 and 950-1000 both in the forward direction, to be sure that the entire gene is sequenced. </br>
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Of the 10 random cultures that were put into liquid LB and left in incubator O.N. on 18/7 only tubes 3 and 9 were viable. We decided to make some more liquid culture of these bacteria and let them incubator at 37°C O.N. </br>
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</br>
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This is to be sure that tomorrow we have enough sample/volume of tube#9 in order to send it off for sequencing.
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                                            <!----------3rd WEEK---------->
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<p> <b>20-07-2012:</b> </p>
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<h2>DNA extraction from O.N. liquid cultures </h2> <br/>
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<p>
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Overnight cultures incubated at 37°C in Ampicilin containing medium:<br/>
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- 10 FFT liquid cultures <br/>
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- 6 SST liquid cultures <br/> <br/>
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The 16 cultures was extracted and a Nanodrop measured the concentrations: <br/>
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Run 3: 116,1 ng/µl <br/>
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Run 9: 10,8 ng/µl (discarded, useless for sequencing at this low concentration)<br/> <br/>
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For the preparation of liquid culture for overnight incubation we marked and transferred single-unit colonies from FFT plates(10) and SST plates(6) to 3mL ampicilin containing liquid medium.
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<br/>
 
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<p> <b>21-07-2012:</b> </p>
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<p> <b>16-07-2012 to 22-07-2012</b> </p>  
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<h2>Gel electrophoresis on extracted cuktures of FFT and SST </h2> <br/>  
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<p>
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We did a cryo “backup” of the liquid cultures from yesterday, containing the FFT and SST genes.
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We still had no 1-SST colonies. Another PCR was made from the original cDNA, using various temperature steps. The pJET vector and 1-SST gene were run on the same gel and purified together on the same spincolumn during gel DNA extraction and mixed the elution buffer with ligation buffer and excess ligase in the final elution step.<br/><br/>
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The 1-SST colonies were incubated at 37C overnight on ampicillin agar medium plates.<br/><br/>
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The bacteria cultures was lysed and the plasmids was extracted using GeneJET Plasmid Miniprep Kit.
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A checkdigest was made on the 10 1-FFT liquid cultures with EcoRI and PstI. The resulting gel had two bands of the expected lengths for vector and insert. These liquid cultures were miniprepped and nanodropped:<br/>
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A Nanodrop analysis was made from our extracted plasmids which should contain our FFT- and SST-gene.
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Tube#3: 138,2ng/µl<br/>
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A gel was constructed and our plasmids was ran through an electrical current at 100V.
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Tube#9: 71,8ng/µl <br/><br/>
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<b>INSERT PICTURE HERE!!!!!!!!</b>
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Tube 3 contained a concentration suitable for sequencing. It was prepared and sent. We used the MWG sites primer design tool (http://www.eurofinsdna.com/) to design primers that anneal to the FFT gene. Seeing as the FFT gene is approximately 1800bp long the primers were designed to anneal between positions 450-500 and 950-1000 both in the forward direction, to be sure that the entire gene is sequenced.<br/><br/>
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The following day 1-SST cultures finaly showed some results, 6 colonies. They were transfered to liquid medium and incubated overnight.<br<br/>/>
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There were no usable results from the gel electrophoresis.  
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The 6 colonies were miniprepped and nanodropped. They all showed concentrations of >60 ng/uL, some even around 160.<br/><br/>
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For future studies we should try to digest the plasmids with the restriction enzymes for a longer period.  
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The following checkdigest showed no usable results.<br/>
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Latest revision as of 02:06, 27 September 2012

iGEM TEAM ::: SDU-DENMARK

Laboratory Notebook

1st week 2nd week 3th week 4th week
5th week 6th week 7th week 8th week
9th week 10th week 11th week 12th week

16-07-2012 to 22-07-2012

We still had no 1-SST colonies. Another PCR was made from the original cDNA, using various temperature steps. The pJET vector and 1-SST gene were run on the same gel and purified together on the same spincolumn during gel DNA extraction and mixed the elution buffer with ligation buffer and excess ligase in the final elution step.

The 1-SST colonies were incubated at 37C overnight on ampicillin agar medium plates.

A checkdigest was made on the 10 1-FFT liquid cultures with EcoRI and PstI. The resulting gel had two bands of the expected lengths for vector and insert. These liquid cultures were miniprepped and nanodropped:
Tube#3: 138,2ng/µl
Tube#9: 71,8ng/µl

Tube 3 contained a concentration suitable for sequencing. It was prepared and sent. We used the MWG sites primer design tool (http://www.eurofinsdna.com/) to design primers that anneal to the FFT gene. Seeing as the FFT gene is approximately 1800bp long the primers were designed to anneal between positions 450-500 and 950-1000 both in the forward direction, to be sure that the entire gene is sequenced.

The following day 1-SST cultures finaly showed some results, 6 colonies. They were transfered to liquid medium and incubated overnight./> The 6 colonies were miniprepped and nanodropped. They all showed concentrations of >60 ng/uL, some even around 160.

The following checkdigest showed no usable results.

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