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<!DOCTYPE html>
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<title>Appendix D: Parent-of-origin effects on transcription and chromatin regulation in reproductive caste determination</title>
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<meta property="og:title" content="Appendix D: Parent-of-origin effects on transcription and chromatin regulation in reproductive caste determination" />
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<meta name="twitter:title" content="Appendix D: Parent-of-origin effects on transcription and chromatin regulation in reproductive caste determination" />
<meta name="author" content="Sean Bresnahan" />
<meta name="date" content="2024-04-11" />
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<li><a href="./">Appendix D</a></li>
<li class="divider"></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About</a></li>
<li class="chapter" data-level="1" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html"><i class="fa fa-check"></i><b>1</b> WGS, mRNA-seq, and ChIP-seq</a>
<ul>
<li class="chapter" data-level="1.1" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#wgs"><i class="fa fa-check"></i><b>1.1</b> WGS</a></li>
<li class="chapter" data-level="1.2" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#mrna-seq"><i class="fa fa-check"></i><b>1.2</b> mRNA-seq</a></li>
<li class="chapter" data-level="1.3" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#chip-seq"><i class="fa fa-check"></i><b>1.3</b> ChIP-seq</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html"><i class="fa fa-check"></i><b>2</b> Transcriptomic Analyses</a>
<ul>
<li class="chapter" data-level="2.1" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html#differential-gene-expression-analysis"><i class="fa fa-check"></i><b>2.1</b> Differential gene expression analysis</a></li>
<li class="chapter" data-level="2.2" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html#wgcna"><i class="fa fa-check"></i><b>2.2</b> WGCNA</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html"><i class="fa fa-check"></i><b>3</b> Allele-Specific Transcriptomic Analyses</a>
<ul>
<li class="chapter" data-level="3.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#snps-and-transcripts"><i class="fa fa-check"></i><b>3.1</b> SNPs and transcripts</a></li>
<li class="chapter" data-level="3.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#poe-gene-lists"><i class="fa fa-check"></i><b>3.2</b> POE gene lists</a></li>
<li class="chapter" data-level="3.3" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#hpf-wl-ql---allelic-transcriptomics"><i class="fa fa-check"></i><b>3.3</b> 192hpf WL & QL - allelic transcriptomics</a>
<ul>
<li class="chapter" data-level="3.3.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-1"><i class="fa fa-check"></i><b>3.3.1</b> Block 1</a></li>
<li class="chapter" data-level="3.3.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-2"><i class="fa fa-check"></i><b>3.3.2</b> Block 2</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#hpf-eggs---allelic-transcriptomics"><i class="fa fa-check"></i><b>3.4</b> 24hpf eggs - allelic transcriptomics</a>
<ul>
<li class="chapter" data-level="3.4.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-3"><i class="fa fa-check"></i><b>3.4.1</b> Block 3</a></li>
<li class="chapter" data-level="3.4.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-4"><i class="fa fa-check"></i><b>3.4.2</b> Block 4</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html"><i class="fa fa-check"></i><b>4</b> ChIP-seq Analysis</a>
<ul>
<li class="chapter" data-level="4.1" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#enrichment-across-promoters-and-gene-bodies"><i class="fa fa-check"></i><b>4.1</b> Enrichment across promoters and gene bodies</a></li>
<li class="chapter" data-level="4.2" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#differential-enrichment-analysis"><i class="fa fa-check"></i><b>4.2</b> Differential enrichment analysis</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k27me3"><i class="fa fa-check"></i><b>4.2.1</b> H3K27me3</a></li>
<li class="chapter" data-level="4.2.2" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k27ac"><i class="fa fa-check"></i><b>4.2.2</b> H3K27ac</a></li>
<li class="chapter" data-level="4.2.3" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k4me3"><i class="fa fa-check"></i><b>4.2.3</b> H3K4me3</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html"><i class="fa fa-check"></i><b>5</b> Allele-Specific ChIP-seq Analyses</a>
<ul>
<li class="chapter" data-level="5.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#snps-and-peaks"><i class="fa fa-check"></i><b>5.1</b> SNPs and peaks</a></li>
<li class="chapter" data-level="5.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#poe-peak-lists"><i class="fa fa-check"></i><b>5.2</b> POE peak lists</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27me3-1"><i class="fa fa-check"></i><b>5.2.1</b> H3K27me3</a></li>
<li class="chapter" data-level="5.2.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27ac-1"><i class="fa fa-check"></i><b>5.2.2</b> H3K27ac</a></li>
<li class="chapter" data-level="5.2.3" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k4me3-1"><i class="fa fa-check"></i><b>5.2.3</b> H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27me3-2"><i class="fa fa-check"></i><b>5.3</b> H3K27me3</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies"><i class="fa fa-check"></i><b>5.3.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.3.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters"><i class="fa fa-check"></i><b>5.3.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27ac-2"><i class="fa fa-check"></i><b>5.4</b> H3K27ac</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies-1"><i class="fa fa-check"></i><b>5.4.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.4.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters-1"><i class="fa fa-check"></i><b>5.4.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k4me3-2"><i class="fa fa-check"></i><b>5.5</b> H3K4me3</a>
<ul>
<li class="chapter" data-level="5.5.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies-2"><i class="fa fa-check"></i><b>5.5.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.5.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters-2"><i class="fa fa-check"></i><b>5.5.2</b> Promoters</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html"><i class="fa fa-check"></i><b>6</b> HPTM-transcription dynamics</a>
<ul>
<li class="chapter" data-level="6.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k27me3-3"><i class="fa fa-check"></i><b>6.1</b> H3K27me3</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-3"><i class="fa fa-check"></i><b>6.1.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.1.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-3"><i class="fa fa-check"></i><b>6.1.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k27ac-3"><i class="fa fa-check"></i><b>6.2</b> H3K27ac</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-4"><i class="fa fa-check"></i><b>6.2.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.2.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-4"><i class="fa fa-check"></i><b>6.2.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k4me3-3"><i class="fa fa-check"></i><b>6.3</b> H3K4me3</a>
<ul>
<li class="chapter" data-level="6.3.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-5"><i class="fa fa-check"></i><b>6.3.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.3.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-5"><i class="fa fa-check"></i><b>6.3.2</b> Promoters</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="7" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html"><i class="fa fa-check"></i><b>7</b> POE HPTM enrichment-POE transcription dynamics</a>
<ul>
<li class="chapter" data-level="7.1" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-1-7"><i class="fa fa-check"></i><b>7.1</b> Block 1</a>
<ul>
<li class="chapter" data-level="7.1.1" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-4"><i class="fa fa-check"></i><b>7.1.1</b> H3K27me3</a></li>
<li class="chapter" data-level="7.1.2" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-4"><i class="fa fa-check"></i><b>7.1.2</b> H3K27ac</a></li>
<li class="chapter" data-level="7.1.3" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-4"><i class="fa fa-check"></i><b>7.1.3</b> H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="7.2" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-2-7"><i class="fa fa-check"></i><b>7.2</b> Block 2</a>
<ul>
<li class="chapter" data-level="7.2.1" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-5"><i class="fa fa-check"></i><b>7.2.1</b> H3K27me3</a></li>
<li class="chapter" data-level="7.2.2" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-5"><i class="fa fa-check"></i><b>7.2.2</b> H3K27ac</a></li>
<li class="chapter" data-level="7.2.3" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-5"><i class="fa fa-check"></i><b>7.2.3</b> H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#logistic-regressions"><i class="fa fa-check"></i><b>7.3</b> Logistic regressions</a>
<ul>
<li class="chapter" data-level="7.3.1" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-6"><i class="fa fa-check"></i><b>7.3.1</b> H3K27me3</a></li>
<li class="chapter" data-level="7.3.2" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-6"><i class="fa fa-check"></i><b>7.3.2</b> H3K27ac</a></li>
<li class="chapter" data-level="7.3.3" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-6"><i class="fa fa-check"></i><b>7.3.3</b> H3K4me3</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="8" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html"><i class="fa fa-check"></i><b>8</b> GO enrichment analyses</a>
<ul>
<li class="chapter" data-level="8.1" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#degs-poe-genes"><i class="fa fa-check"></i><b>8.1</b> DEGs & POE genes</a></li>
<li class="chapter" data-level="8.2" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#wgcna-modules"><i class="fa fa-check"></i><b>8.2</b> WGCNA modules</a></li>
<li class="chapter" data-level="8.3" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#hptm-differentially-enriched-regions"><i class="fa fa-check"></i><b>8.3</b> HPTM differentially enriched regions</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html"><i class="fa fa-check"></i><b>9</b> POE gene feature assessment</a>
<ul>
<li class="chapter" data-level="9.1" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#spatial-clustering"><i class="fa fa-check"></i><b>9.1</b> Spatial clustering</a></li>
<li class="chapter" data-level="9.2" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-length-and-recombination-rates"><i class="fa fa-check"></i><b>9.2</b> Intron length and recombination rates</a>
<ul>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#recombination-rate"><i class="fa fa-check"></i>Recombination rate</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron"><i class="fa fa-check"></i>% intron</a></li>
</ul></li>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Appendix D: Parent-of-origin effects on transcription and chromatin regulation in reproductive caste determination</a>
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<h1 class="title">Appendix D: Parent-of-origin effects on transcription and chromatin regulation in reproductive caste determination</h1>
<p class="author"><em>Sean Bresnahan</em></p>
<p class="date"><em>2024-04-11</em></p>
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<h1>About<a href="index.html#about" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<center>
Supplementary information for Chapter 5 of
<br>
<br>
<br>
<strong>MOLECULAR MECHINISMS OF PHENOTYPIC VARIATION</strong>
<strong>IN HONEY BEES (<em>APIS MELLIFERA</em>)</strong>
<br>
<br>
<br>
A Dissertation in <br>
Molecular, Cellular, and Integrative Biosciences <br>
by <br>
Sean T. Bresnahan <br>
<br>
<br>
© 2024 Sean T. Bresnahan <br>
<br>
<br>
Submitted in Partial Fulfillment <br>
of the Requirements <br>
for the Degree of <br>
<br>
<br>
Doctor of Philosophy <br>
<br>
<br>
The Pennsylvania State University <br>
The Graduate School <br>
<br>
<br>
May 2024
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