Skip to content

Commit

Permalink
Build site.
Browse files Browse the repository at this point in the history
  • Loading branch information
@EugOT
EugOT committed Apr 23, 2023
1 parent 53dce73 commit 2c3fddc
Show file tree
Hide file tree
Showing 10 changed files with 1,925 additions and 410 deletions.
151 changes: 114 additions & 37 deletions docs/about.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

<title>About</title>

<script src="site_libs/header-attrs-2.16/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
Expand Down Expand Up @@ -188,25 +188,18 @@
border-radius: 4px;
}

.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}

.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "&#xe258;";
border: none;
}

.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
content: "\e258";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
border: none;
}

.tabset-dropdown > .nav-tabs > li.active {
Expand Down Expand Up @@ -262,8 +255,26 @@
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="dynamic_oc3-pop.html">Glutamate and GABA dynamic in Onecut3 neurons</a>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Analysis

<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="dynamic_oc3-pop.html">Glutamate and GABA dynamic in Onecut3 neurons</a>
</li>
<li>
<a href="onecuts-affected-cells.html">Onecut3 affected cells</a>
</li>
<li>
<a href="onecut3wotrh.html">Glutamate and GABA dynamic in LHA Onecut3 neurons</a>
</li>
<li>
<a href="onecut.html">Glutamate and GABA dynamic in LHA neurons</a>
</li>
</ul>
</li>
<li>
<a href="about.html">About</a>
Expand Down Expand Up @@ -312,7 +323,7 @@ <h1 class="title toc-ignore">About</h1>
<div class="tab-content">
<div id="summary" class="tab-pane fade in active">
<p>
<strong>Last updated:</strong> 2022-10-04
<strong>Last updated:</strong> 2023-04-23
</p>
<p>
<strong>Checks:</strong> <span
Expand Down Expand Up @@ -359,15 +370,15 @@ <h1 class="title toc-ignore">About</h1>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomHarkanyLabZupancic2022tree7f4395e4f4cb168c983224a3994056371dc9a604targetblank7f4395ea">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomHarkanyLabZupancic2022tree53dce73ea70b319cbb3a6a981710a4396cf1fb38targetblank53dce73a">
<span class="glyphicon glyphicon-ok text-success"
aria-hidden="true"></span> <strong>Repository version:</strong>
<a href="https://github.com/Harkany-Lab/Zupancic_2022/tree/7f4395e4f4cb168c983224a3994056371dc9a604" target="_blank">7f4395e</a>
<a href="https://github.com/Harkany-Lab/Zupancic_2022/tree/53dce73ea70b319cbb3a6a981710a4396cf1fb38" target="_blank">53dce73</a>
</a>
</p>
</div>
<div
id="strongRepositoryversionstrongahrefhttpsgithubcomHarkanyLabZupancic2022tree7f4395e4f4cb168c983224a3994056371dc9a604targetblank7f4395ea"
id="strongRepositoryversionstrongahrefhttpsgithubcomHarkanyLabZupancic2022tree53dce73ea70b319cbb3a6a981710a4396cf1fb38targetblank53dce73a"
class="panel-collapse collapse">
<div class="panel-body">
<p>
Expand All @@ -377,7 +388,7 @@ <h1 class="title toc-ignore">About</h1>
</p>
<p>
The results in this page were generated with repository version
<a href="https://github.com/Harkany-Lab/Zupancic_2022/tree/7f4395e4f4cb168c983224a3994056371dc9a604" target="_blank">7f4395e</a>.
<a href="https://github.com/Harkany-Lab/Zupancic_2022/tree/53dce73ea70b319cbb3a6a981710a4396cf1fb38" target="_blank">53dce73</a>.
See the <em>Past versions</em> tab to see a history of the changes made
to the R Markdown and HTML files.
</p>
Expand All @@ -392,27 +403,11 @@ <h1 class="title toc-ignore">About</h1>
</p>
<pre><code>
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: data/oc3_fin.h5seurat
Ignored: data/rar2020.srt.cont.oc2or3.raw.h5seurat

Unstaged changes:
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Gad1_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Gad2_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Nav1_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Nav2_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Onecut2_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Slc17a6_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Slc32a1_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Th_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Trh_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Trio_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Slc32a1-Onecut3_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Slc32a1-Th_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Slc32a1-Trh_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Th-Onecut3_.pdf
Modified: output/figures/stat-corr-plt_oc3-rna-data-Th-Trh_.pdf

</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not
Expand Down Expand Up @@ -458,6 +453,41 @@ <h1 class="title toc-ignore">About</h1>
<tbody>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://github.com/Harkany-Lab/Zupancic_2022/blob/53dce73ea70b319cbb3a6a981710a4396cf1fb38/analysis/about.Rmd" target="_blank">53dce73</a>
</td>
<td>
Evgenii O. Tretiakov
</td>
<td>
2023-04-23
</td>
<td>
update README and missing notebooks from an old repository for the
submission
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://rawcdn.githack.com/Harkany-Lab/Zupancic_2022/d06bf756235d75292e5b43475b549fecff4ca06f/docs/about.html" target="_blank">d06bf75</a>
</td>
<td>
Evgenii O. Tretiakov
</td>
<td>
2022-10-04
</td>
<td>
Build site. Redraw figures.
</td>
</tr>
<tr>
<td>
html
</td>
<td>
Expand Down Expand Up @@ -548,7 +578,54 @@ <h1 class="title toc-ignore">About</h1>
</div>
</div>
</div>
<p>Describe your project.</p>
<div
id="glutamate-and-gaba-neurons-share-cascading-onecut3nav2-driven-differentiation-trajectories-in-the-developing-hypothalamus"
class="section level1">
<h1>Glutamate and GABA neurons share cascading Onecut3/NAV2-driven
differentiation trajectories in the developing hypothalamus</h1>
<p>This repository contains code and output of the analysis of
single-nuclei RNA sequencing data for the article <a
href="https://doi.org/" title="Zupancic M et al., 2023">Zupancic M et
al., 2023</a>.</p>
<p>Please see file <code>CITATION</code> in the root of your Git repo
that contains the citation information.</p>
<p>To see the results of the analysis please visit the <a
href="https://harkany-lab.github.io/Zupancic_2023/index.html"
title="Analysis website">analysis website</a></p>
<div id="rationale" class="section level2">
<h2>Rationale:</h2>
<p>Differentiation trajectories to generate specialized cellular
features rely on sets of transcription factors (TFs) whose temporal
dynamics and coexistence underlie morphological and neurochemical
divergence among neurons and neuroendocrine cells. Even though
transcriptional programs were extensively studied in the developing
nervous system, the coupling of TFs to effector gene networks that time
and shape the morphogenesis of these polarized cells is less known.</p>
</div>
<div id="results" class="section level2">
<h2>Results:</h2>
<p>Here, we make the curious observation that evolutionarily conserved
Onecut3, a subordinate in the Onecut TF family known to control fate
selection in progenitors, is instead expressed in fate-restricted
neuroblasts in the vertebrate hypothalamus. In particular, a pool of
Ascl1-containing progenitors in the midgestational mouse hypothalamus
gives rise to both GABA and glutamate neurons destined to the
periventricular and lateral hypothalamus, respectively, which uniformly
upregulate Onecut3 only when exiting the proliferative zone of the 3rd
ventricle. By combining single-cell RNA-seq, genetic Onecut3 reporters,
gain-of-function models in vitro, and loss-of-function analysis in early
developing mice and C. elegans, we identify that Onecut3 instructs
neuronal differentiation and maturation, through a Navigator-2 pathway
to modulate neuritogenesis and leading process motility.</p>
</div>
<div id="conclusion" class="section level2">
<h2>Conclusion:</h2>
<p>Onecut3 executes an unexpected function by inducing cytoskeletal
modifications of key importance for neuronal maturation and network
integration during the morphogenesis of many neuronal phenotypes in the
vertebrate hypothalamus.</p>
</div>
</div>


<!-- Adjust MathJax settings so that all math formulae are shown using
Expand Down
Loading

0 comments on commit 2c3fddc

Please sign in to comment.