latest updates

index.Rmd

@@ -1,64 +1,63 @@
----
-title: "Index"
-date: "`r Sys.Date()`"
-author:
-  - name: Arun Seetharam
-    affiliation: Tuteja Lab
-    affiliation_url: https://www.tutejalab.org
-output:
-  #pdf_document: default
-  rmdformats::readthedown:
-    self_contained: true
-    thumbnails: false
-    lightbox: true
-    gallery: true
-    highlight: tango
----
-
-```{r setup, include=FALSE}
-options(max.print = "125")
-knitr::opts_chunk$set(
-  echo = TRUE,
-  collapse = TRUE,
-  comment = "#>",
-  fig.path = "assets/",
-  fig.width = 8,
-  prompt = FALSE,
-  tidy = FALSE,
-  message = FALSE,
-  warning = TRUE
-)
-knitr::opts_knit$set(width = 75)
-```
-
-# Mouse Trophoblast smallRNAseq analyses
-
-Performed  at [Tuteja Lab](https://www.tutejalab.org), Iowa State University, Ames IA-50011
-
-### Documentation
-
-The Wiki for the entire analyses is provided in this R-markdown files [`1_smallRNAseq.Rmd`](1_smallRNAseq.Rmd) and [`2_proteomics.Rmd`](2_proteomics.Rmd). The rendered html file is accessible on this link:
-
-1. [Small RNAseq analyses](https://tuteja-lab.github.io/mouse.trophoblast.smallRNAseq/1_smallRNAseq.html)
-2. [Proteomics analyses](https://tuteja-lab.github.io/mouse.trophoblast.smallRNAseq/2_proteomics.html)
-
-### Data availability
-
-* Small RNAseq data available for download upon publication from NCBI GEO [GSE222855](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE222855)
-* Proteomics data available for download upon pulication from [Massive UCSD repository](http://massive.ucsd.edu/ProteoSAFe/status.jsp?task=35b93125f20f40ebbae166e5f8657860)
-
-### Contacts
-
-1. Project related questions: Geetu Tuteja
-2. Scripts and workflow related questions: please open an [issue](https://github.com/Tuteja-Lab/mouse.trophoblast.smallRNAseq/issues/new) here on GitHub.
-
-
-### Publication
-
-If you use the scripts from this repository in your research, please cite this publication:
-
-_coming soon_
-
-Kinkade, J. A., Seetharam, A. S., Sachdev, S., Bivens, N. J., Phinney, B. S., Grigorean, G., Roberts, R. M., Tuteja, G., Rosenfeld, C. S., Extracellular Vesicle Contents of Mouse Trophoblast Cells and Their Predicted Influence on Fetal Brain Development _(in preparation)_
-
-
+---
+title: "Index"
+date: "`r Sys.Date()`"
+author:
+  - name: Arun Seetharam
+    affiliation: Tuteja Lab
+    affiliation_url: https://www.tutejalab.org
+output:
+  #pdf_document: default
+  rmdformats::readthedown:
+    self_contained: true
+    thumbnails: false
+    lightbox: true
+    gallery: true
+    highlight: tango
+---
+
+```{r setup, include=FALSE}
+options(max.print = "125")
+knitr::opts_chunk$set(
+  echo = TRUE,
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "assets/",
+  fig.width = 8,
+  prompt = FALSE,
+  tidy = FALSE,
+  message = FALSE,
+  warning = TRUE
+)
+knitr::opts_knit$set(width = 75)
+```
+
+# Mouse Trophoblast smallRNAseq analyses
+
+Performed  at [Tuteja Lab](https://www.tutejalab.org), Iowa State University, Ames IA-50011
+
+### Documentation
+
+The Wiki for the entire analyses is provided in this R-markdown files [`1_smallRNAseq.Rmd`](1_smallRNAseq.Rmd), [`2_proteomics.Rmd`](2_proteomics.Rmd) and [`3_bulkRNAseq.Rmd`](3_bulkRNAseq.Rmd). The rendered html file is accessible on this link:
+
+1. [Small RNAseq analyses](https://tuteja-lab.github.io/mouse.trophoblast.smallRNAseq/1_smallRNAseq.html)
+2. [Proteomics analyses](https://tuteja-lab.github.io/mouse.trophoblast.smallRNAseq/2_proteomics.html)
+3. [Bulk RNAseq analyses](https://tuteja-lab.github.io/mouse.trophoblast.smallRNAseq/3_bulkRNAseq.html)
+
+### Data availability
+
+* Small RNAseq data available for download upon publication from NCBI GEO [GSE222855](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE222855)
+* Proteomics data available for download upon pulication from [Massive UCSD repository](http://massive.ucsd.edu/ProteoSAFe/status.jsp?task=35b93125f20f40ebbae166e5f8657860)
+
+### Contacts
+
+1. Project related questions: Geetu Tuteja
+2. Scripts and workflow related questions: please open an [issue](https://github.com/Tuteja-Lab/mouse.trophoblast.smallRNAseq/issues/new) here on GitHub.
+
+
+### Publication
+
+If you use the scripts from this repository in your research, please cite this publication:
+
+Jessica A Kinkade, Arun S Seetharam, Shrikesh Sachdev, Nathan J Bivens, Brett S Phinney, Gabriela Grigorean, R Michael Roberts, Geetu Tuteja, Cheryl S Rosenfeld, Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta–brain axis, Biology of Reproduction, Volume 110, Issue 2, February 2024, Pages 310–328, DOI: [10.1093/biolre/ioad146](https://doi.org/10.1093/biolre/ioad146)
+
+