http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&action=history Revision history for this page on the wiki en MediaWiki 1.13.2 Sun, 19 May 2013 06:15:00 GMT http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=681209&oldid=prev <p><span class="autocomment">Part 1: Bird microbiome analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:30, 6 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Part 1: Bird microbiome analysis===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Part 1: Bird microbiome analysis===</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">&lt;font color=red&gt;done!&lt;/font color&gt;</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Overview====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Overview====</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 81:</td> <td colspan="2" class="diff-lineno">Line 79:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>You are welcome to get together with your clone ### partner for this next part, or if you really want to you can work alone from each other's text files and Excel write-ups -- but that's twice the work!</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>You are welcome to get together with your clone ### partner for this next part, or if you really want to you can work alone from each other's text files and Excel write-ups -- but that's twice the work!</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;font color=red&gt;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Updates for W/F section:</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* When adding your sequences to an existing T/R alignment file, you may need to first ''Insert Blank Sequence'', and then copy-paste into that slot.</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Some T/R ### pairs finished entirely, and in other cases only one person out of the pair was able to finish aligning their sequences. You can add to either a full or a half T/R alignment file, but just keep track of what data you are using. Be sure also to post your own .mas file, which the other T/R person can then add to and re-post.</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;/font color&gt;</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Open MEGA. In the upper left corner, click on the icon labeled ''Align'', and choose ''Edit/Build Alignment'' from the pulldown menu. This selection should open the Alignment Explorer. When you are prompted, choose &quot;DNA&quot; alignment of course.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Open MEGA. In the upper left corner, click on the icon labeled ''Align'', and choose ''Edit/Build Alignment'' from the pulldown menu. This selection should open the Alignment Explorer. When you are prompted, choose &quot;DNA&quot; alignment of course.</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Wed, 06 Mar 2013 14:30:43 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680834&oldid=prev <p><span class="autocomment">Part 2: Microsporidia primer analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:05, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 111:</td> <td colspan="2" class="diff-lineno">Line 111:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border=&quot;1&quot;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border=&quot;1&quot;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Lane &nbsp;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Lane &nbsp;</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!Sample (<del class="diffchange diffchange-inline">X </del>&amp;mu;L)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!Sample (<ins class="diffchange diffchange-inline">20 </ins>&amp;mu;L)</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!Lane</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!Lane</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!Sample (<del class="diffchange diffchange-inline">Y </del>&amp;mu;L)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!Sample (<ins class="diffchange diffchange-inline">20 </ins>&amp;mu;L)</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 1 &nbsp;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 1 &nbsp;</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 18:05:18 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680833&oldid=prev <p><span class="autocomment">Part 2: Microsporidia primer analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:04, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 103:</td> <td colspan="2" class="diff-lineno">Line 103:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Part 2: Microsporidia primer analysis===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Part 2: Microsporidia primer analysis===</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">&lt;font color&gt;Sample order/gel prep will be written up Mon evening or Tue morning&lt;/font color&gt;</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The 60 PCR samples were labeled numerically, and the associated sample definitions are included in the [[Media: S13-M1D7-PCR-calcs.xlsx | attached file]]. Each group should have three consecutive reactions; note that #1-12 are reference samples (with V1-PMP2 primer set) that will be added to the gel by the teaching faculty.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The 60 PCR samples were labeled numerically, and the associated sample definitions are included in the [[Media: S13-M1D7-PCR-calcs.xlsx | attached file]]. Each group should have three consecutive reactions; note that #1-12 are reference samples (with V1-PMP2 primer set) that will be added to the gel by the teaching faculty.</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 18:04:57 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680832&oldid=prev <p><span class="autocomment">Part 2: Microsporidia primer analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:04, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 106:</td> <td colspan="2" class="diff-lineno">Line 106:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;font color&gt;Sample order/gel prep will be written up Mon evening or Tue morning&lt;/font color&gt;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;font color&gt;Sample order/gel prep will be written up Mon evening or Tue morning&lt;/font color&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The 60 PCR samples were labeled numerically, and the associated sample definitions are included in the attached file. Each group should have three consecutive reactions; note that #1-12 are reference samples (with V1-PMP2 primer set) that will be added to the gel by the teaching faculty.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The 60 PCR samples were labeled numerically, and the associated sample definitions are included in the <ins class="diffchange diffchange-inline">[[Media: S13-M1D7-PCR-calcs.xlsx | </ins>attached file<ins class="diffchange diffchange-inline">]]</ins>. Each group should have three consecutive reactions; note that #1-12 are reference samples (with V1-PMP2 primer set) that will be added to the gel by the teaching faculty.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Each gel will have the following general structure for sample loading:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Each gel will have the following general structure for sample loading:</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 198:</td> <td colspan="2" class="diff-lineno">Line 198:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;/center&gt;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;/center&gt;</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Sample preparation: mix by pipetting, take 20 &amp;mu;L, add 2.5 &amp;mu;L loading dye, then load 20 &amp;mu;L onto gel.</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;br style=&quot;clear:both;&quot;/&gt;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;br style=&quot;clear:both;&quot;/&gt;</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 18:04:41 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680732&oldid=prev <p><span class="autocomment">Part 2: Microsporidia primer analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 02:54, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 141:</td> <td colspan="2" class="diff-lineno">Line 141:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 10</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 10</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Group 2, sample 2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Group 2, sample 2</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|}</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;/center&gt;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;br style=&quot;clear:both;&quot;/&gt;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">It's essential that the correct reference sample be run on each gel, and therefore that groups requiring the same reference sample pair up. Let the table below be your guide:</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;center&gt;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">{| border=&quot;1&quot;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Gel number</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Reference samples</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Group 1</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Group 2</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| T/R 1 </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Specificity (VC, EH, mixture)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Red</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Orange</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| T/R 2</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Specificity (VC, EH, mixture)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Blue</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Purple</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| T/R 3</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Sensitivity (VC: lo, mid, hi)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Yellow</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Green</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| T/R 4</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Sensitivity (VC: lo, mid, hi)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Pink</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Plat runs W/F Red!</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| W/F 1 </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Specificity (VC, EH, mixture)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Orange</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Green</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| W/F 2</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Specificity (VC, EH, mixture)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Blue </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Pink</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| W/F 3</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Sensitivity (EH: lo, mid, hi)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Yellow</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Purple</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| W/F 4</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Sensitivity (EH: lo, mid, hi)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Platinum</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Red runs T/R Platinum!</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 02:54:13 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680731&oldid=prev <p><span class="autocomment">Part 2: Microsporidia primer analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 02:45, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 117:</td> <td colspan="2" class="diff-lineno">Line 117:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!Sample (Y &amp;mu;L)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!Sample (Y &amp;mu;L)</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| 1 Group 1, sample 1</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| 1 &nbsp;</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">| </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">| </ins>Group 1, sample 1</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 6</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 6</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| V1-PMP2, sample 2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| V1-PMP2, sample 2</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 02:45:02 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680730&oldid=prev <p><span class="autocomment">Part 2: Microsporidia primer analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 02:44, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 105:</td> <td colspan="2" class="diff-lineno">Line 105:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;font color&gt;Sample order/gel prep will be written up Mon evening or Tue morning&lt;/font color&gt;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;font color&gt;Sample order/gel prep will be written up Mon evening or Tue morning&lt;/font color&gt;</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The 60 PCR samples were labeled numerically, and the associated sample definitions are included in the attached file. Each group should have three consecutive reactions; note that #1-12 are reference samples (with V1-PMP2 primer set) that will be added to the gel by the teaching faculty.</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Each gel will have the following general structure for sample loading:</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;center&gt;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">{| border=&quot;1&quot;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Lane </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">!Sample (X &amp;mu;L)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">!Lane</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">!Sample (Y &amp;mu;L)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 1 Group 1, sample 1</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 6</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| V1-PMP2, sample 2</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 2 </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|&nbsp; Group 1, sample 2</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 7</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| V1-PMP2, sample 3</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 3 </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Group 1, sample 3</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 8</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Group 2, sample 1</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 4 </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|&nbsp; [http://www.neb.com/nebecomm/products/productN3231.asp DNA ladder] (load 10 &amp;mu;L) </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 9</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Group 2, sample 2</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 5 </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| V1-PMP2, sample 1</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| 10</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">| Group 2, sample 2</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|}</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;/center&gt;</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;br style=&quot;clear:both;&quot;/&gt;</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==For next time==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==For next time==</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 02:44:47 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680727&oldid=prev <p><span class="autocomment">Reagent list</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 02:40, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 114:</td> <td colspan="2" class="diff-lineno">Line 114:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reagent list==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reagent list==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">write something here or not accessible to edit</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Mostly your brains!</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Agarose gels</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**2:1 mixture of high-resolution:standard agarose</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**Prepared in TAE buffer</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**With SYBR Safe stain (Invitrogen)</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">***used at manufacturer's recommended concentration, 10000-fold dilution</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Loading dye</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**0.25% xylene cyanol</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**30% glycerol</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**RNase</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Gels made and run in 1X TAE buffer</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**40 mM Tris</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**20 mM Acetic Acid </ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**1 mM EDTA, pH 8.3</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*100 bp DNA ladder from New England BioLabs</ins></div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 02:40:22 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680726&oldid=prev <p><span class="autocomment">For next time</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 02:39, 5 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 108:</td> <td colspan="2" class="diff-lineno">Line 108:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==For next time==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==For next time==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">#</del>Some of you have journal clubs next time. No other required homework is due on Day 8.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Some of you have journal clubs next time. No other required homework is due on Day 8.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#The following bonus assignment may be submitted on Day 8: Prepare a figure and caption for your [[20.109%28S13%29:_Primer_design_summary | primer design summary]] that shows your raw PCR results -- the agarose gel. (Later you might decide to process this data in some way, but not necessarily.) Write an early draft of the accompanying main text paragraph.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#The following bonus assignment may be submitted on Day 8: Prepare a figure and caption for your [[20.109%28S13%29:_Primer_design_summary | primer design summary]] that shows your raw PCR results -- the agarose gel. (Later you might decide to process this data in some way, but not necessarily.) Write an early draft of the accompanying main text paragraph.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Tue, 05 Mar 2013 02:39:35 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29 http://openwetware.org/index.php?title=20.109%28S13%29:Phylogenetic_analysis_%28Day7%29&diff=680696&oldid=prev <p><span class="autocomment">Part 1: Bird microbiome analysis</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 21:53, 4 March 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Part 1: Bird microbiome analysis===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Part 1: Bird microbiome analysis===</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&lt;font color=red&gt;<del class="diffchange diffchange-inline">Done except for possible changes to Part 1E</del>&lt;/font color&gt;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&lt;font color=red&gt;<ins class="diffchange diffchange-inline">done!</ins>&lt;/font color&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Overview====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Overview====</div></td></tr> <!-- diff generator: internal 2013-05-19 06:15:00 --> </table> Mon, 04 Mar 2013 21:53:37 GMT AgiStachowiak http://openwetware.org/wiki/Talk:20.109%28S13%29:Phylogenetic_analysis_%28Day7%29