https://gcat.davidson.edu/GcatWiki/index.php?action=history&feed=atom&title=DM_Notes_1.28.16DM Notes 1.28.16 - Revision history2026-05-17T15:08:14ZRevision history for this page on the wikiMediaWiki 1.28.2https://gcat.davidson.edu/GcatWiki/index.php?title=DM_Notes_1.28.16&diff=17923&oldid=prevDymaghini at 19:47, 28 January 20162016-01-28T19:47:51Z<p></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 19:47, 28 January 2016</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">Placeholder</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Reads are nearly all 72 bp. We want to know what genes they're associated with, and how many of that gene there are in a particular sample. </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">'''Some challenges ahead:''' </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">How do you count the number of genes and compare across time points? What is the standard procedure? There aren't the same number of reads in every sample. Could normalize to a particular housekeeping gene. (2 people)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">How do we know we have the right tissue? Serosa, mucosa, cross section. We can find a gene that we know is expressed only in a certain tissue subset. What can we do now? We have the fastQC reports- can BLAST the overrepresented sequences in the report. We don't know what they are, but a BLAST could give us some hints (8 people will work on that). </ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Campbell has gone ahead and asked Todd Castoe for the supplementary gene names from the paper that identified ~2000 differentially expressed intestinal genes.</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">SRP151827 - link to NCBI repository of all of their reads. Lots of links and tools, but we're not entirely sure how to navigate. (2 people)</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Someone needs to go through the gene names list, and change "protein of unknown function" to numbered/different names, so there aren't duplicates. Find any other duplicates, and rename and number.(4 people)</ins></div></td></tr>
</table>Dymaghinihttps://gcat.davidson.edu/GcatWiki/index.php?title=DM_Notes_1.28.16&diff=17911&oldid=prevDymaghini: Created page with "Placeholder"2016-01-28T18:34:44Z<p>Created page with "Placeholder"</p>
<p><b>New page</b></p><div>Placeholder</div>Dymaghini