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Harkany-Lab · Jul 25, 2024 · 78f7fe4 · 78f7fe4
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diff --git a/analysis/_site.yml b/analysis/_site.yml
@@ -1,21 +1,30 @@
-name: "Cinquina_2024"
+name: "Cinquina et al., 2024"
 output_dir: ../docs
 navbar:
-  title: "Cinquina_2024"
+  title: "Cinquina et al., 2024"
   left:
-  - text: Home
-    href: index.html
-  - text: Analysis
-    menu:
-      - text: MTT assay analysis of EDA-treated astrocytes
-        href: MTT.html
-  - text: About
-    href: about.html
-  - text: License
-    href: license.html
+    - text: Home
+      href: index.html
+    - text: About
+      href: about.html
+    - text: Analysis
+      menu:
+        - text: MTT assay analysis of EDA-treated astrocytes
+          href: MTT.html
+        - text: Exploratory analysis of CaCyBP and S100a6 expression in embryonic mice cortex dataset with focus on astrocytic lineage
+          href: cortex_visualisation.html
+    - text: "Methods"
+        href: methods.html
+  right:
+    - text: "License"
+      href: license.html
+    - icon: fa-github
+      href: https://github.com/Harkany-Lab/Cinquina_2024
 output:
   workflowr::wflow_html:
     toc: yes
     toc_float: yes
     theme: cosmo
     highlight: textmate
+    code_folding: hide
+    df_print: paged
diff --git a/analysis/about.Rmd b/analysis/about.Rmd
@@ -5,6 +5,40 @@ output:
     toc: false
 editor_options:
   chunk_output_type: console
+bibliography:
+    - "`r here::here('data/references/references.bib')`"
 ---
 
-Describe your project.
+# Astrocytes modulate neuronal development by S100A6 signaling
+
+This repository contains code and output of the analysis of single-cell RNA sequencing data and experimental results for the article [Cinquina V et al., 2024][publication].
+
+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][website].
+
+## Purpose:
+
+We aimed to investigate the role of astrocyte-derived factors in regulating neuronal morphogenesis during brain development. Specifically, we hypothesized that S100A6, a Ca²⁺-binding protein expressed by astrocytes, could act as a gliotransmitter to modulate neuronal development through its interaction with calcyclin-binding protein (CaCyBP) in neurons.
+
+## Results:
+
+1. S100A6 is specifically expressed in astrocytes during late embryonic and early postnatal development of the mouse cortex.
+2. CaCyBP, the binding partner of S100A6, is expressed in neurons during the same developmental period.
+3. S100A6 is released by astrocytes in response to glutamate and eicosapentaenoic acid (EPA) stimulation.
+4. Exogenous S100A6 inhibits neurite outgrowth and reduces CaCyBP levels in neurons.
+5. CaCyBP regulates protein turnover in neurons through the unfolded protein response (UPR) pathway.
+6. Maternal diet, particularly EPA intake, influences S100A6-CaCyBP signaling in the developing fetal brain.
+
+## Conclusions:
+
+Our results describe a novel molecular axis of astrocyte-neuron communication, which is unique in limiting neuronal morphogenesis through the ER/UPS pathway. S100A6 acts as an astrocyte-specific gliotransmitter, which regulates neuronal proteostasis through CaCyBP. This signaling pathway is sensitive to environmental factors, particularly maternal nutrition during pregnancy.
+
+## Data and Code Availability:
+
+Raw data were obtained from the Single Cell Portal [@tarhanSingleCellPortal2023; @dibellaMolecularLogicCellular2021]. All generated data are available in this repository.
+
+The code for the analysis is available at https://github.com/harkany-lab/Cinquina_2024.
+
+[publication]: https://doi.org/ "Cinquina V et al., 2024"
+[website]: https://harkany-lab.github.io/Cinquina_2024/index.html "Analysis website"
diff --git a/analysis/index.Rmd b/analysis/index.Rmd
@@ -6,6 +6,82 @@ output:
     toc: false
 editor_options:
   chunk_output_type: console
+bibliography:
+    - "`r here::here('data/references/references.bib')`"
 ---
 
-Welcome to my research website.
+Welcome to the analysis website for the manuscript "Astrocytes modulate
+neuronal development by S100A6 signaling". This site contains the code
+and detailed methods used in our study.
+
+1.  System requirements
+
+-   All software dependencies and operating systems (including version
+    numbers) are available in the [methods
+    section](methods.html "Methods section of the analysis website")
+-   This analysis has been tested on x86_64-pc-linux-gnu (64-bit)
+    platform running under Ubuntu 22.04.1 LTS
+-   The analysis is performed within a Docker container, which can be
+    obtained from Docker Hub
+
+2.  Installation guide
+
+-   To reproduce the analysis environment, pull the Docker image using:
+
+    ```         
+    docker pull etretiakov/workbench-session-complete:jammy-2024.06.19-custom-12.8
+    ```
+
+-   Typical pull time on a standard desktop computer with good internet
+    connection should be within 30 minutes
+
+3.  Data availability
+
+-   Raw data were obtained from the Single Cell Portal
+    [@tarhanSingleCellPortal2023; @dibellaMolecularLogicCellular2021]
+-   All generated data are available in this repository
+
+4.  Analysis reproduction
+
+-   To reproduce the analysis and figures, use the following command
+    within the Docker container:
+
+``` r
+workflowr::wflow_publish(
+ c(
+   "analysis/index.Rmd",
+   "analysis/methods.Rmd",
+   "analysis/cortex_visualisation.Rmd",
+   "analysis/MTT.Rmd"
+ ),
+ message = "Reproduce analysis site",
+ project = "."
+)
+```
+
+This command will:
+
+1.  Publish the main index page, methods page, cortical development
+    analysis, and MTT assay analysis.
+2.  Use the commit message "Reproduce analysis site".
+3.  Assume the current working directory is the project root (specified
+    by `project = "."`).
+
+Make sure to run this command from within your Docker container to
+ensure all dependencies are available. You may need to adjust the file
+paths if your R Markdown files are located in a different directory
+within your project structure.
+
+-   Expected run time for full analysis reproduction on a resonably
+    powerful cluster node or workstation is within several hours
+
+5.  Additional resources
+
+-   [Seurat analysis of cortical
+    development](cortex_visualisation.html "Cortical development analysis")
+-   [MTT assay analysis](MTT.html "MTT assay analysis")
+-   [Full methods
+    description](methods.html "Methods section of the analysis website")
+
+For any questions or issues, please open an issue on the [GitHub
+repository](https://github.com/harkany-lab/Cinquina_2024).
diff --git a/analysis/license.Rmd b/analysis/license.Rmd
@@ -3,19 +3,37 @@ title: "License"
 output:
   workflowr::wflow_html:
     toc: false
+    theme: cosmo
+    highlight: textmate
+    code_folding: hide
+    df_print: paged
 editor_options:
   chunk_output_type: console
 ---
 
-What license are you using for your code? See [choosealicense.com][choose] for
-help deciding. It's a convention to save a file `LICENSE` in the root of your
-Git repo that contains the license text.
+This repository contains code and output of the analysis of single-nuclei
+RNA sequencing data for the article [Cinquina V et al., 2023][publication].
 
-What license are you using for the written content on your site? It is
-traditional to choose a [Creative Commons][cc] license for this type of content.
 
-[choose]: https://choosealicense.com/
-[cc]: https://creativecommons.org/choose/
+Please see file `CITATION` in the root of your Git repo that contains 
+the citation information.
 
-How should others cite your work? It's a convention to save a 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][website].
+
+
+The code in this analysis is covered by the
+[GNU General Public License v3.0][gpl] and the written content on this website
+is covered by a [Creative Commons CC-BY][cc] license.
+
+
+The publications mentioned and datasets used are covered by their respective 
+licenses and usage agreements. Please refer to those sources for details.
+
+
+
+[publication]: https://doi.org/ "Cinquina V et al., "
+[website]: https://harkany-lab.github.io/Hevesi_2023/index.html "Analysis website"
+[gpl]: https://choosealicense.com/licenses/gpl-3.0/ "GPL-3.0 License"
+[cc]: https://creativecommons.org/licenses/by/4.0/ "CC-BY License"