Team:Exeter/lab book/novpol/wk8
From 2012.igem.org
Jamesml213 (Talk | contribs) |
|||
(13 intermediate revisions not shown) | |||
Line 22: | Line 22: | ||
<font face="Verdana" color="#57b947" size="2"> | <font face="Verdana" color="#57b947" size="2"> | ||
- | + | <!--Project Division Links--> | |
- | <a href="https://2012.igem.org/Team:Exeter/lab_book/1gp/wk1"; style="color:#57b947">Single Gene Plasmids and Enzyme Characterisation</a> | + | <a href="https://2012.igem.org/Team:Exeter/lab_book/proto"; style="color:#57b947">Protocols</a> |
- | + | | | |
- | + | <a href="https://2012.igem.org/Team:Exeter/lab_book/1gp/wk1"; style="color:#57b947">Single Gene Plasmids and Enzyme Characterisation</a> | |
- | + | | | |
- | + | <a href="https://2012.igem.org/Team:Exeter/lab_book/novpol/wk1"; style="color:#57b947">Showcasing Polysaccharide Production</a> | |
- | + | | | |
- | + | <a href="https://2012.igem.org/Team:Exeter/lab_book/3gip/wk1"; style="color:#57b947">The 3-Gene Inducible Plasmid</a> | |
- | + | <p> | |
- | + | <a href="https://2012.igem.org/Team:Exeter/lab_book/gibs/wk1"; style="color:#57b947">Operon Construction</a> | |
- | + | | | |
- | + | <a href="https://2012.igem.org/Team:Exeter/lab_book/glyco/wk1"; style="color:#57b947">Glycobase</a> | |
+ | </p> | ||
+ | <!--End Project Division Links--> | ||
+ | |||
</font> | </font> | ||
Line 42: | Line 45: | ||
<td rowspan="2" valign="top" align="center" width="170"> | <td rowspan="2" valign="top" align="center" width="170"> | ||
- | + | <!--Project Division Week Hyperlinks--> | |
<div style="text-align:center; width:170"> | <div style="text-align:center; width:170"> | ||
<font face="Verdana" color="#1d1d1b" size="2"> | <font face="Verdana" color="#1d1d1b" size="2"> | ||
Line 54: | Line 57: | ||
</p> | </p> | ||
<a href="https://2012.igem.org/Team:Exeter/lab_book/novpol/wk3"; style="color:#1d1d1b">23rd - 27th July</a> | <a href="https://2012.igem.org/Team:Exeter/lab_book/novpol/wk3"; style="color:#1d1d1b">23rd - 27th July</a> | ||
- | |||
- | |||
- | |||
- | |||
<p> | <p> | ||
- | - | ||
Line 81: | Line 80: | ||
- | - | ||
</p> | </p> | ||
- | <a href="https://2012.igem.org/Team:Exeter/ | + | <a href="https://2012.igem.org/Team:Exeter/Results/showcase"; style="color:#e30614" target="_blank"><font size="3"><b>Results</b></font></a> |
+ | </font> | ||
</font> | </font> | ||
</div> | </div> | ||
Line 104: | Line 104: | ||
<!------------ENTER LAB BOOK HERE: PLEASE INCLUDE DATES WITHIN THE WEEK------------> | <!------------ENTER LAB BOOK HERE: PLEASE INCLUDE DATES WITHIN THE WEEK------------> | ||
- | <p>**<b>Tuesday | + | <p>**<b>Tuesday 28/08/12</b>**</p><br> |
<p><b>9.30am</b></p> | <p><b>9.30am</b></p> | ||
Line 165: | Line 165: | ||
</TABLE> | </TABLE> | ||
+ | <p><b>10.00am</b></p> | ||
+ | <p><a href="https://2012.igem.org/Team:Exeter/lab_book/proto/4" style="color:#57b947"><u>3A Assembly</u></a></p> | ||
+ | <TABLE BORDER="3" ALIGN="CENTRE" WIDTH="50%" CELLPADDING="4" CELLSPACING="3"> | ||
- | <p> | + | <TR ALIGN="CENTER"> |
+ | <TH><b>Sample</b></TH> | ||
+ | <TH><b>Conc of DNA (ng/μl)</b></TH> | ||
+ | <TH><b>DNA required (μl)</b></TH> | ||
+ | <TH><b>Water required (μl)</b></TH> | ||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Cyc 2</b></TH> | ||
+ | <TD>150</TD> | ||
+ | <TD>3.3</TD> | ||
+ | <TD>13.5</TD> | ||
+ | </TR> | ||
+ | |||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>HAS 1</b></TH> | ||
+ | <TD>330</TD> | ||
+ | <TD>5.5</TD> | ||
+ | <TD>11.3</TD> | ||
+ | </TR> | ||
+ | |||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>SacB 2</b></TH> | ||
+ | <TD>100</TD> | ||
+ | <TD>5.0</TD> | ||
+ | <TD>11.8</TD> | ||
+ | </TR> | ||
+ | </TABLE> | ||
+ | |||
+ | <TABLE BORDER="3" ALIGN="CENTRE" WIDTH="50%" CELLPADDING="4" CELLSPACING="3"> | ||
+ | |||
+ | <TR> | ||
+ | <TH COLSPAN="2"><BR><H4>Upstream</H4></TH> | ||
+ | </TR> | ||
+ | |||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>DNA</b></TH> | ||
+ | <TD>500ng</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>BUFFER (10x)</b></TH> | ||
+ | <TD>2μl</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>BSA (100x)</b></TH> | ||
+ | <TD>0.2μl</TD> | ||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Water</b></TH> | ||
+ | <TD>up to 20μl total V</TD> | ||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>ENZYME 1 - ECORI</b></TH> | ||
+ | <TD>0.5μL</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>ENZYME 2 - SpeI</b></TH> | ||
+ | <TD>0.5μL</TD> | ||
+ | </TR> | ||
+ | <TR> | ||
+ | <TH COLSPAN="2"><BR><H4>Downstream</H4></TH> | ||
+ | </TR> | ||
+ | |||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>DNA</b></TH> | ||
+ | <TD>500ng</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>BUFFER (10x)</b></TH> | ||
+ | <TD>2μl</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>BSA (100x)</b></TH> | ||
+ | <TD>0.2μl</TD> | ||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Water</b></TH> | ||
+ | <TD>up to 20μl total V</TD> | ||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>ENZYME 1 - XbaI</b></TH> | ||
+ | <TD>0.5μL</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>ENZYME 2 - PstI</b></TH> | ||
+ | <TD>0.5μL</TD> | ||
+ | </TR> | ||
+ | <TR> | ||
+ | <TH COLSPAN="2"><BR><H4>Chloramphenicol Plasmid</H4></TH> | ||
+ | </TR> | ||
+ | |||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>DNA</b></TH> | ||
+ | <TD>500ng</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>BUFFER (10x)</b></TH> | ||
+ | <TD>2μl</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>BSA (100x)</b></TH> | ||
+ | <TD>0.2μl</TD> | ||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Water</b></TH> | ||
+ | <TD>up to 20μl total V</TD> | ||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>ENZYME 1 - ECORI</b></TH> | ||
+ | <TD>0.5μL</TD> | ||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>ENZYME 2 - PstI</b></TH> | ||
+ | <TD>0.5μL</TD> | ||
+ | </TR> | ||
+ | |||
+ | </TABLE> | ||
+ | <br> | ||
+ | <p><b>11.00am</b></p> | ||
<p>Incubated for 1 hour 37°C</p> | <p>Incubated for 1 hour 37°C</p> | ||
+ | <p><b>12.00pm</b></p> | ||
<p>Put samples into wells of 80°C to heat denature enzymes. </p> | <p>Put samples into wells of 80°C to heat denature enzymes. </p> | ||
- | <p> | + | <br> |
+ | <p><b>1.30pm</b></p> | ||
+ | |||
+ | |||
<p>Created gel.</p> | <p>Created gel.</p> | ||
<p>Ran gel electrophoresis, 150mV for ~20 minutes.</p> | <p>Ran gel electrophoresis, 150mV for ~20 minutes.</p> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2012/3/32/Exe2012_28-08-12_cyc_has_sacb.jpg" alt="" title="" width="550" height="413"><br> | ||
<p>Weighed eppendorf before and after addition of sliced gel portion containing DNA.</p> | <p>Weighed eppendorf before and after addition of sliced gel portion containing DNA.</p> | ||
<p>Re-separated DNA from gel</p> | <p>Re-separated DNA from gel</p> | ||
- | < | + | <p><b>4.00pm</b></p> |
+ | <p>Ligation process.</p> | ||
+ | |||
+ | <TABLE BORDER="3" ALIGN="CENTRE" WIDTH="50%" CELLPADDING="4" CELLSPACING="3"> | ||
+ | |||
+ | <TR> | ||
+ | <TH COLSPAN="2"><BR><H4>Ligation</H4></TH> | ||
+ | </TR> | ||
+ | |||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Backbone</b></TH> | ||
+ | <TD>2μl</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Upstream</b></TH> | ||
+ | <TD>2μl</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Downstream</b></TH> | ||
+ | <TD>2μl</TD> | ||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>DNA ligase buffer</b></TH> | ||
+ | <TD>1μl</TD> | ||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>DNA ligase enzyme</b></TH> | ||
+ | <TD>0.5μL</TD> | ||
+ | |||
+ | |||
+ | |||
+ | </TR> | ||
+ | <TR ALIGN="CENTER"> | ||
+ | <TH><b>Water</b></TH> | ||
+ | <TD>2.5μL</TD> | ||
+ | </TR> | ||
+ | </TABLE> | ||
+ | |||
+ | |||
+ | <p>Plasmid + Upstream + Downstream</p> | ||
+ | <p>PSBC13 + Cyc2 + Term</p> | ||
+ | <p>PSBC13 + HAS1 +Term</p> | ||
+ | <p>PSBC13 + SacB2 + Term</p> | ||
+ | <br> | ||
+ | <p>Ligations left at 4°C overnight.</p> | ||
+ | |||
<p>**<b>Wednesday 29/08/12</b>**</p><br> | <p>**<b>Wednesday 29/08/12</b>**</p><br> | ||
<p><b>2.00pm</p></b> | <p><b>2.00pm</p></b> | ||
- | <p>Transformations.</p> | + | <p><a href="https://2012.igem.org/Team:Exeter/lab_book/proto/1" style="color:#57b947"><u>Transformations</u></a>.</p> |
<ul>* pSB1C3 cyclodextrin </ul> | <ul>* pSB1C3 cyclodextrin </ul> | ||
<ul>* pSB1C3 hyaluronan synthase </ul> | <ul>* pSB1C3 hyaluronan synthase </ul> | ||
Line 219: | Line 435: | ||
<p><b>4.30pm</b></p> | <p><b>4.30pm</b></p> | ||
+ | <p><a href="https://2012.igem.org/Team:Exeter/lab_book/proto/2" style="color:#57b947"><u>Transferred cultures to liquid medium</u></a></p> | ||
<p>Made up liquid broth using plates: | <p>Made up liquid broth using plates: | ||
<ul>* pSB1C3 cyclodextrin </ul> | <ul>* pSB1C3 cyclodextrin </ul> | ||
Line 236: | Line 453: | ||
<p>**<b>Friday 31/08/12</b>**</p><br> | <p>**<b>Friday 31/08/12</b>**</p><br> | ||
- | <p>9.30am</p></b> | + | <p><b>9.30am</p></b> |
+ | <p><a href="http://www.fermentas.com/templates/files/tiny_mce/coa_pdf/coa_k0502.pdf" style="color:#57b947" target="_blank"><u>Mini-Prep</u></a></p> | ||
<p>Liquid broth transferred to new containers – leaving pipette tip behind.</p> | <p>Liquid broth transferred to new containers – leaving pipette tip behind.</p> | ||
<p>These were then centrifuged at 3900rpg for 10 minutes.</p> | <p>These were then centrifuged at 3900rpg for 10 minutes.</p> | ||
Line 253: | Line 471: | ||
<b><p>12.30am</p></b> | <b><p>12.30am</p></b> | ||
<p>Samples were then placed on the NanoDrop machine to get the concentration of DNA.</p> | <p>Samples were then placed on the NanoDrop machine to get the concentration of DNA.</p> | ||
- | <p>Using this and the measurements from the previous digestion, | + | <p>Using this and the measurements from the previous digestion, Table 2, the amount of DNA and water required for all samples could be calculated.</p> <br> |
Line 300: | Line 518: | ||
</TABLE> | </TABLE> | ||
<br> | <br> | ||
- | <p> | + | <p>Amount of DNA and water required for all samples: </p><br> |
<TABLE BORDER="3" ALIGN="CENTER" WIDTH="50%" CELLPADDING="4" CELLSPACING="3"> | <TABLE BORDER="3" ALIGN="CENTER" WIDTH="50%" CELLPADDING="4" CELLSPACING="3"> | ||
Line 500: | Line 718: | ||
<p>Samples out of incubator. 4μl of Loading Buffer added to each. These were then transferred to individual wells. </p> | <p>Samples out of incubator. 4μl of Loading Buffer added to each. These were then transferred to individual wells. </p> | ||
<p>LADDDER – HAS+Term 1,2,3,4 – CYC+Term 1,2,3,4 – WbiP 2, 3, 4 </p> | <p>LADDDER – HAS+Term 1,2,3,4 – CYC+Term 1,2,3,4 – WbiP 2, 3, 4 </p> | ||
- | <p>Next | + | <p>Next row contains: LADDER – SacB+Term 1,2,3,4 – HAS 1,2,3,4 – CYC 1,2,4,</p> |
<img src="https://static.igem.org/mediawiki/2012/6/6c/Exe2012_HasT_cycT_wbip_sacT_has_cyc.JPG" alt="" title="" width="550" height="467"> | <img src="https://static.igem.org/mediawiki/2012/6/6c/Exe2012_HasT_cycT_wbip_sacT_has_cyc.JPG" alt="" title="" width="550" height="467"> | ||
Line 516: | Line 734: | ||
</table> | </table> | ||
+ | |||
+ | <table width="980" align="center" cellspacing="20"> | ||
+ | <tr align="center"> | ||
+ | <td> | ||
+ | <font color="#57B947" size="1" face="Verdana"> | ||
+ | <p><u>Website Designed and Built by: Ryan Edginton, James Lynch & Alex Clowsley</u> | | ||
+ | <a href="https://igem.org/Team.cgi?id=764" style="color:#57B947" target="_blank"><u>Contact Us</u></a> | | ||
+ | <a href="https://2012.igem.org/Team:Exeter/site_map" style="color:#57B947"><u>Site Map</u></a></p> | ||
+ | </font> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
</body> | </body> | ||
</html> | </html> |
Latest revision as of 23:59, 26 September 2012
Showcasing Polysaccharide Production: 27th - 31st August 2012 **Tuesday 28/08/12** 9.30am Using the NanoDrop Spectrophotometer the DNA concentrations of Becca Philp’s samples were checked for accuracy.
10.00am
11.00am Incubated for 1 hour 37°C 12.00pm Put samples into wells of 80°C to heat denature enzymes. 1.30pm Created gel. Ran gel electrophoresis, 150mV for ~20 minutes. Weighed eppendorf before and after addition of sliced gel portion containing DNA. Re-separated DNA from gel 4.00pm Ligation process.
Plasmid + Upstream + Downstream PSBC13 + Cyc2 + Term PSBC13 + HAS1 +Term PSBC13 + SacB2 + Term Ligations left at 4°C overnight. **Wednesday 29/08/12** 2.00pm
Equilibrated water bath to 42°C. SOC medium kept at room temperature. One Shot TOP10 competent cells, stored at -80°C. 1. Thawed One Shot TOP10 vials on ice for transformation.
2.15pm
2.45pm
3.15pm
4.15pm Span all samples at 3000G for 2 minutes. Took 90μl off of each vial, this was then discarded. Pipette mixed leftover contents of each eppendorf. Using aseptic technique the rest was spread onto plates. 5.15pm These were then put in an incubator overnight (~16+hours) at 37°C. **Thursday 30/08/12** 9.30am Checked plates. Colonies have formed on all. These were then all placed in the fridge, 4°C. 4.30pm Transferred cultures to liquid medium Made up liquid broth using plates:
4x made per plate – aseptic technique Used 10ml broth 10μl chloramphenicol Scraped off single colony using pipette tip which is then ejected into liquid broth. 5.30pm Put into horizontal shaker set at 37°C, 220rpm – left overnight.
**Friday 31/08/12** 9.30am Liquid broth transferred to new containers – leaving pipette tip behind. These were then centrifuged at 3900rpg for 10 minutes. 1. supernatant discarded leaving pellet at the base.
12.30am Samples were then placed on the NanoDrop machine to get the concentration of DNA. Using this and the measurements from the previous digestion, Table 2, the amount of DNA and water required for all samples could be calculated.
Amount of DNA and water required for all samples:
All samples were spun down. 2.45pm Incubated all tubes for digestion period of 1 hour. 3.55pm Samples out of incubator. 4μl of Loading Buffer added to each. These were then transferred to individual wells. LADDDER – HAS+Term 1,2,3,4 – CYC+Term 1,2,3,4 – WbiP 2, 3, 4 Next row contains: LADDER – SacB+Term 1,2,3,4 – HAS 1,2,3,4 – CYC 1,2,4, |
Website Designed and Built by: Ryan Edginton, James Lynch & Alex Clowsley | Contact Us | Site Map |