From 2c3fddc95ca93ffbae2d64bd73436d5b842de523 Mon Sep 17 00:00:00 2001 From: "Evgenii O. Tretiakov" Date: Sun, 23 Apr 2023 15:03:29 +0000 Subject: [PATCH] Build site. --- docs/about.html | 151 ++- docs/index.html | 149 ++- docs/license.html | 150 ++- .../fonts/glyphicons-halflings-regular.svg | 574 ++++---- .../header-attrs-2.21/header-attrs.js | 12 + docs/site_libs/jquery-3.6.0/jquery-3.6.0.js | 2 + .../jquery-3.6.0/jquery-3.6.0.min.js | 2 +- .../jquery-3.6.0/jquery-3.6.0.min.map | 2 +- .../pagedtable-1.1/css/pagedtable.css | 142 ++ .../site_libs/pagedtable-1.1/js/pagedtable.js | 1151 +++++++++++++++++ 10 files changed, 1925 insertions(+), 410 deletions(-) create mode 100644 docs/site_libs/header-attrs-2.21/header-attrs.js create mode 100644 docs/site_libs/pagedtable-1.1/css/pagedtable.css create mode 100644 docs/site_libs/pagedtable-1.1/js/pagedtable.js diff --git a/docs/about.html b/docs/about.html index 645fa1b..3417c6c 100644 --- a/docs/about.html +++ b/docs/about.html @@ -13,7 +13,7 @@ About - + @@ -188,8 +188,8 @@ 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; @@ -197,16 +197,9 @@ } .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { - content: ""; - 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 { @@ -262,8 +255,26 @@
  • Home
    • -
  • - Glutamate and GABA dynamic in Onecut3 neurons +
  • + +
  • About @@ -312,7 +323,7 @@

    About

    -Last updated: 2022-10-04 +Last updated: 2023-04-23

    Checks: About

    - + Repository version: -7f4395e +53dce73

    @@ -377,7 +388,7 @@

    About

    The results in this page were generated with repository version -7f4395e. +53dce73. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

    @@ -392,27 +403,11 @@

    About

    
 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
-

    Note that any generated files, e.g. HTML, png, CSS, etc., are not @@ -458,6 +453,41 @@

    About

    +Rmd + + +53dce73 + + +Evgenii O. Tretiakov + + +2023-04-23 + + +update README and missing notebooks from an old repository for the +submission + + + + +html + + +d06bf75 + + +Evgenii O. Tretiakov + + +2022-10-04 + + +Build site. Redraw figures. + + + + html @@ -548,7 +578,54 @@

    About

    -

    Describe your project.

    +
    +

    Glutamate and GABA neurons share cascading Onecut3/NAV2-driven +differentiation trajectories in the developing hypothalamus

    +

    This repository contains code and output of the analysis of +single-nuclei RNA sequencing data for the article Zupancic M et +al., 2023.

    +

    Please see file CITATION in the root of your Git repo +that contains the citation information.

    +

    To see the results of the analysis please visit the analysis website

    +
    +

    Rationale:

    +

    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.

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    +
    +

    Results:

    +

    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.

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    +
    +

    Conclusion:

    +

    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.

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    +
    @@ -188,8 +191,8 @@ 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; @@ -197,16 +200,9 @@ } .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { - content: ""; - 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 { @@ -233,6 +229,9 @@ + @@ -262,8 +261,26 @@
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  • - Glutamate and GABA dynamic in Onecut3 neurons +
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  • About @@ -281,6 +298,14 @@