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<atom:link href="https://robertslab.github.io/sams-notebook/index.xml" rel="self" type="application/rss+xml"/>
<description></description>
<generator>quarto-1.3.450</generator>
<lastBuildDate>Tue, 02 Jan 2024 08:00:00 GMT</lastBuildDate>
<lastBuildDate>Wed, 03 Jan 2024 08:00:00 GMT</lastBuildDate>
<item>
<title>Data Exploration - CEABIGR Spurious Transcription Calculations and Plotting</title>
<dc:creator>Sam White</dc:creator>
<link>https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/index.html</link>
<description><![CDATA[




<section id="intro" class="level1">
<h1>Intro</h1>
<p>As part of the <a href="https://github.com/sr320/ceabigr">CEABIGR project</a> (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change in exon expression, relative to Exon 1, for each gene in a single sample. The decision to perform the calculation in this manner was based on <span class="citation" data-cites="li2018">(Li et al. 2018)</span>. I took the next steps to perform this across all samples, as well as generate some comparison plots. After this, will explore how spurious transcription relates to methylation levels across genes.</p>
<p>See <a href="https://github.com/sr320/ceabigr/blob/8bc64a3a5dcca6932d14bcf13a3fb15f3e9d5d95/code/65-exon-coverage.qmd"><code>65-exon-coverage.qmd</code></a> for code.</p>
<div class="callout callout-style-default callout-note callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
Note
</div>
</div>
<div class="callout-body-container callout-body">
<p>Code and plots link to commit <code>8bc64a3</code>.</p>
</div>
</div>
</section>
<section id="plots" class="level1">
<h1>Plots</h1>
<p>All plots are line plots of the mean natural log fold-change in exon expression (Exons 2-6), relative to Exon 1. Black bars represent standard error.</p>
<div class="callout callout-style-default callout-note callout-titled">
<div class="callout-header d-flex align-content-center">
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Note
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<p>Plots are simply arranged side-by-side. Scales of axes are <em>not</em> intended to match.</p>
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<p><img src="https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/https:/raw.githubusercontent.com/sr320/ceabigr/8bc64a3a5dcca6932d14bcf13a3fb15f3e9d5d95/output/65-exon-coverage/figures/control-females.v.control-males-line_plot.png" class="img-fluid" alt="Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control females. Blue line is control males. Black bars represent standard error."></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
<p><img src="https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/https:/raw.githubusercontent.com/sr320/ceabigr/8bc64a3a5dcca6932d14bcf13a3fb15f3e9d5d95/output/65-exon-coverage/figures/control-females.v.exposed-females-line_plot.png" class="img-fluid" alt="Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control females. Blue line is exposed females. Black bars represent standard error."></p>
</div>
</div>
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
<p><img src="https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/https:/raw.githubusercontent.com/sr320/ceabigr/8bc64a3a5dcca6932d14bcf13a3fb15f3e9d5d95/output/65-exon-coverage/figures/control-males.v.exposed-males-line_plot.png" class="img-fluid" alt="Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control males. Blue line is exposed males. Black bars represent standard error."></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
<p><img src="https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/https:/raw.githubusercontent.com/sr320/ceabigr/8bc64a3a5dcca6932d14bcf13a3fb15f3e9d5d95/output/65-exon-coverage/figures/controls.v.exposed-line_plot.png" class="img-fluid" alt="Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is controls. Blue line is exposed. Black bars represent standard error."></p>
</div>
</div>
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
<p><img src="https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/https:/raw.githubusercontent.com/sr320/ceabigr/8bc64a3a5dcca6932d14bcf13a3fb15f3e9d5d95/output/65-exon-coverage/figures/exposed-females.v.exposed-males-line_plot.png" class="img-fluid" alt="Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is exposed females. Blue line is exposed males. Black bars represent standard error."></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
<p><img src="https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/https:/raw.githubusercontent.com/sr320/ceabigr/8bc64a3a5dcca6932d14bcf13a3fb15f3e9d5d95/output/65-exon-coverage/figures/females.v.males-line_plot.png" class="img-fluid" alt="Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is females. Blue line is males. Black bars represent standard error."></p>
</div>
</div>
</div>



</section>

<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents"><h2 class="anchored quarto-appendix-heading">References</h2><div id="refs" class="references csl-bib-body hanging-indent">
<div id="ref-li2018" class="csl-entry">
Li, Yong, Yi Jin Liew, Guoxin Cui, Maha J. Cziesielski, Noura Zahran, Craig T. Michell, Christian R. Voolstra, and Manuel Aranda. 2018. <span>“DNA Methylation Regulates Transcriptional Homeostasis of Algal Endosymbiosis in the Coral Model Aiptasia.”</span> <em>Science Advances</em> 4 (8). <a href="https://doi.org/10.1126/sciadv.aat2142">https://doi.org/10.1126/sciadv.aat2142</a>.
</div>
</div></section></div> ]]></description>
<category>2024</category>
<category>CEABIGR</category>
<category>plot</category>
<category>Eastern oyster</category>
<category>Crassostrea virginica</category>
<guid>https://robertslab.github.io/sams-notebook/posts/2024/2024-01-03-Data-Exploration---CEABIGR-Spurious-Transcription-Calculations-and-Plotting/index.html</guid>
<pubDate>Wed, 03 Jan 2024 08:00:00 GMT</pubDate>
</item>
<item>
<title>Daily Bits - January 2024</title>
<dc:creator>Sam White</dc:creator>
Expand Down Expand Up @@ -11982,162 +12069,5 @@ font-style: inherit;">&gt;&gt;</span> system_path.log</span></code></pre></div>
<guid>https://robertslab.github.io/sams-notebook/posts/2023/2023-07-27-DIAMOND-BLASTx---C.virginica-Genes-on-Mox/index.html</guid>
<pubDate>Fri, 28 Jul 2023 04:00:00 GMT</pubDate>
</item>
<item>
<title>qPCR - C.gigas polyIC</title>
<dc:creator>Sam White</dc:creator>
<link>https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/index.html</link>
<description><![CDATA[




<p>Using <a href="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-21-Reverse-Transcription---C.gigas-PolyIC-RNA/">cDNA from 20230721</a>, performed qPCR on the following <a href="https://github.com/RobertsLab/resources/issues/1686">primer sets selected by Steven</a> (GitHub Issue), along with <code>Cg_Actin</code> as a potential normalizing gene:</p>
<table class="table">
<thead>
<tr class="header">
<th>SRID</th>
<th>Primer</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>1170/1</td>
<td>Cg_Actin</td>
</tr>
<tr class="even">
<td>1830/1</td>
<td>Cg_DICER</td>
</tr>
<tr class="odd">
<td>1172/3</td>
<td>Cg_GAPDH</td>
</tr>
<tr class="even">
<td>1832/3</td>
<td>Cg_IRF2</td>
</tr>
<tr class="odd">
<td>1834/5</td>
<td>Cg_SACSIN</td>
</tr>
<tr class="even">
<td>1828/9</td>
<td>Cg_VIPERIN</td>
</tr>
<tr class="odd">
<td>1826/7</td>
<td>Cg_cGAS</td>
</tr>
<tr class="even">
<td>1383/4</td>
<td>Cg_citrate_synthase</td>
</tr>
</tbody>
</table>
<p>qPCR calcs:</p>
<ul>
<li><a href="https://docs.google.com/spreadsheets/d/1yZYj3LSSEYbcXVd6PXT39CG9bsIX73LfnfqcaotHdH8/edit?usp=sharing">20230726 - qPCR Calcs polyIC gigas cDNA</a> (Google Sheet)</li>
</ul>
<p>Reactions were run on white, low-profile, 96-well qPCR plates (USA Scientific). A total of two plates were run. One was run on a CFC Connect (BioRad) and the other on a CFX96 (BioRad). See the qPCR Report in the RESULTS section below for cycling params, plate layouts, etc.</p>
<p>All samples were run in <em>singular</em>. Normally duplicates/triplicates are run. However, due to time and sample constraints, samples were just run in <em>singular</em>. No template controls were run in duplicate.</p>
<hr>
<section id="results" class="level1">
<h1>RESULTS</h1>
<p>Brief note(s) on results:</p>
<ul>
<li>Samples <code>T2</code> and <code>T15</code> seem to come up earlier than all other samples in almost all of the primer sets.</li>
</ul>
<p>qPCR Results file (CSV)</p>
<ul>
<li><a href="https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Quantification%20-Cq-Results.csv">sam_2023-07-26_13-06-28_Connect-Quantification%20-Cq-Results.csv</a></li>
</ul>
<p>qPCR Data file (QPCRD - CFX Maestro required)</p>
<ul>
<li><a href="https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2023-07-26_13-06-28_Connect.pcrd">sam_2023-07-26_13-06-28_Connect.pcrd</a></li>
</ul>
<p>qPCR Report (PDF)</p>
<ul>
<li><a href="https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2023-07-26_13-06-28_Connect.pdf">sam_2023-07-26_13-06-28_Connect.pdf</a></li>
</ul>
<hr>
<section id="plots" class="level4">
<h4 class="anchored" data-anchor-id="plots">PLOTS</h4>
<table class="table">
<colgroup>
<col style="width: 2%">
<col style="width: 6%">
<col style="width: 46%">
<col style="width: 44%">
</colgroup>
<thead>
<tr class="header">
<th>SRID</th>
<th>Primer</th>
<th>Amplification Plot</th>
<th>Melt Curve</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>1170/1</td>
<td>Cg_Actin</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_Actin-amp-plots.png" class="img-fluid" alt="Cg_Actin amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_Actin-melt-plots.png" class="img-fluid" alt="Cg_Actin melt plot"></td>
</tr>
<tr class="even">
<td>1830/1</td>
<td>Cg_DICER</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_DICER-amp-plots.png" class="img-fluid" alt="Cg_DICER amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_DICER-melt-plots.png" class="img-fluid" alt="Cg_DICER melt plot"></td>
</tr>
<tr class="odd">
<td>1172/3</td>
<td>Cg_GAPDH</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_GAPDH-amp-plots.png" class="img-fluid" alt="Cg_GAPDH amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_GAPDH-melt-plots.png" class="img-fluid" alt="Cg_GAPDH melt plot"></td>
</tr>
<tr class="even">
<td>1832/3</td>
<td>Cg_IRF2</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_IRF2-amp-plots.png" class="img-fluid" alt="Cg_IRF2 amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_IRF2-melt-plots.png" class="img-fluid" alt="Cg_IRF2 melt plot"></td>
</tr>
<tr class="odd">
<td>1834/5</td>
<td>Cg_SACSIN</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_SACSIN-amp-plots.png" class="img-fluid" alt="Cg_SACSIN amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_SACSIN-melt-plots.png" class="img-fluid" alt="Cg_SACSIN melt plot"></td>
</tr>
<tr class="even">
<td>1828/9</td>
<td>Cg_VIPERIN</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_VIPERIN-amp-plots.png" class="img-fluid" alt="Cg_VIPERIN amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_VIPERIN-melt-plots.png" class="img-fluid" alt="Cg_VIPERIN melt plot"></td>
</tr>
<tr class="odd">
<td>1826/7</td>
<td>Cg_cGAS</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_cGAS-amp-plots.png" class="img-fluid" alt="Cg_cGAS amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_cGAS-melt-plots.png" class="img-fluid" alt="Cg_cGAS melt plot"></td>
</tr>
<tr class="even">
<td>1383/4</td>
<td>Cg_citrate_synthase</td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_citrate_synthase-amp-plots.png" class="img-fluid" alt="Cg_citrate_synthase amplification plot"></td>
<td><img src="https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/https:/owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_citrate_synthase-melt-plots.png" class="img-fluid" alt="Cg_citrate_synthase melt plot"></td>
</tr>
</tbody>
</table>


</section>
</section>

]]></description>
<category>2023</category>
<category>Miscellaneous</category>
<guid>https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/index.html</guid>
<pubDate>Wed, 26 Jul 2023 18:42:00 GMT</pubDate>
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