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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<meta charset="utf-8" />
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<title>S4 ChIP-seq Analysis | Supplementary Materials</title>
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<meta property="og:title" content="S4 ChIP-seq Analysis | Supplementary Materials" />
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<meta name="twitter:title" content="S4 ChIP-seq Analysis | Supplementary Materials" />
<meta name="author" content="Sean T. Bresnahan, Shaun Mahony, Kate Anton, Brock Harpur, Christina M. Grozinger" />
<meta name="date" content="2024-05-07" />
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<body>
<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
<div class="book-summary">
<nav role="navigation">
<ul class="summary">
<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>
<li class="chapter" data-level="5.6" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#combined-results"><i class="fa fa-check"></i><b>5.6</b> Combined results</a>
<ul>
<li class="chapter" data-level="5.6.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#block-1-7"><i class="fa fa-check"></i><b>5.6.1</b> Block 1</a></li>
<li class="chapter" data-level="5.6.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#block-2-7"><i class="fa fa-check"></i><b>5.6.2</b> Block 2</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-1-8"><i class="fa fa-check"></i><b>7.1</b> Block 1</a>
<ul>
<li class="chapter" data-level="" 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>H3K27me3</a></li>
<li class="chapter" data-level="" 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>H3K27ac</a></li>
<li class="chapter" data-level="" 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>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-2-8"><i class="fa fa-check"></i><b>7.2</b> Block 2</a>
<ul>
<li class="chapter" data-level="" 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>H3K27me3</a></li>
<li class="chapter" data-level="" 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>H3K27ac</a></li>
<li class="chapter" data-level="" 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>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-regression"><i class="fa fa-check"></i><b>7.3</b> Logistic regression</a>
<ul>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-gene-body"><i class="fa fa-check"></i>H3K27me3 (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-promoter"><i class="fa fa-check"></i>H3K27me3 (promoter)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-gene-body"><i class="fa fa-check"></i>H3K27ac (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-promoter"><i class="fa fa-check"></i>H3K27ac (promoter)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-gene-body"><i class="fa fa-check"></i>H3K4me3 (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-promoter"><i class="fa fa-check"></i>H3K4me3 (promoter)</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>
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<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>
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<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-feature-analyses"><i class="fa fa-check"></i><b>9.2</b> Intron feature analyses</a>
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<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>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-gc"><i class="fa fa-check"></i>Intron GC</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-cpg-density"><i class="fa fa-check"></i>Intron CpG density</a></li>
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<div id="chip-seq-analysis" class="section level1 hasAnchor" number="4">
<h1><span class="header-section-number">S4</span> ChIP-seq Analysis<a href="chip-seq-analysis.html#chip-seq-analysis" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="enrichment-across-promoters-and-gene-bodies" class="section level2 hasAnchor" number="4.1">
<h2><span class="header-section-number">4.1</span> Enrichment across promoters and gene bodies<a href="chip-seq-analysis.html#enrichment-across-promoters-and-gene-bodies" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div class="float">
<img src="resources/figures/peakProfs.png" alt="Frequency and distribution of HPTM peaks across gene bodies (a-c) and 5kb regions centered around transcription start sites (TSS) (d-f) in worker-destined larvae (WL) and queen-destined larvae (QL) at 192hpf. 95% confidence intervals are indicated." />
<div class="figcaption">Frequency and distribution of HPTM peaks across gene bodies (a-c) and 5kb regions centered around transcription start sites (TSS) (d-f) in worker-destined larvae (WL) and queen-destined larvae (QL) at 192hpf. 95% confidence intervals are indicated.</div>
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<div id="differential-enrichment-analysis" class="section level2 hasAnchor" number="4.2">
<h2><span class="header-section-number">4.2</span> Differential enrichment analysis<a href="chip-seq-analysis.html#differential-enrichment-analysis" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Descriptive statistics of windows and regions assessed for differential HPTM enrichment.</p>
<table>
<thead>
<tr>
<th style="text-align:left;">
HPTM
</th>
<th style="text-align:right;">
Windows
</th>
<th style="text-align:right;">
Windows after filtering
</th>
<th style="text-align:right;">
Percent of total
</th>
<th style="text-align:right;">
Merged regions
</th>
<th style="text-align:right;">
Mean region length
</th>
<th style="text-align:right;">
SD region length
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
H3K27me3
</td>
<td style="text-align:right;">
1472315
</td>
<td style="text-align:right;">
712081
</td>
<td style="text-align:right;">
48.36
</td>
<td style="text-align:right;">
30778
</td>
<td style="text-align:right;">
4635
</td>
<td style="text-align:right;">
2875
</td>
</tr>
<tr>
<td style="text-align:left;">
H3K27ac
</td>
<td style="text-align:right;">
1472072
</td>
<td style="text-align:right;">
702892
</td>
<td style="text-align:right;">
47.75
</td>
<td style="text-align:right;">
31993
</td>
<td style="text-align:right;">
4469
</td>
<td style="text-align:right;">
2808
</td>
</tr>
<tr>
<td style="text-align:left;">
H3K4me3
</td>
<td style="text-align:right;">
1471353
</td>
<td style="text-align:right;">
712097
</td>
<td style="text-align:right;">
48.40
</td>
<td style="text-align:right;">
32518
</td>
<td style="text-align:right;">
4451
</td>
<td style="text-align:right;">
2817
</td>
</tr>
</tbody>
</table>
<div id="h3k27me3" class="section level3 hasAnchor" number="4.2.1">
<h3><span class="header-section-number">4.2.1</span> H3K27me3<a href="chip-seq-analysis.html#h3k27me3" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li><a href="resources/data/H3K27me3_csaw_merged2.csv">H3K27me3 - csaw results table</a></li>
<li><a href="resources/data/H3K27me3_DERs2_genes.bed">H3K27me3 - genes in differentially enriched regions</a></li>
</ul>
</div>
<div id="h3k27ac" class="section level3 hasAnchor" number="4.2.2">
<h3><span class="header-section-number">4.2.2</span> H3K27ac<a href="chip-seq-analysis.html#h3k27ac" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li><a href="resources/data/H3K27ac_csaw_merged2.csv">H3K27ac - csaw results table</a></li>
<li><a href="resources/data/H3K27ac_DERs2_genes.bed">H3K27ac - genes in differentially enriched regions</a></li>
</ul>
</div>
<div id="h3k4me3" class="section level3 hasAnchor" number="4.2.3">
<h3><span class="header-section-number">4.2.3</span> H3K4me3<a href="chip-seq-analysis.html#h3k4me3" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li><a href="resources/data/H3K4me3_csaw_merged2.csv">H3K4me3 - csaw results table</a></li>
<li><a href="resources/data/H3K4me3_DERs2_genes.bed">H3K4me3 - genes in differentially enriched regions</a></li>
</ul>
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