Add citation info

README.Rmd

@@ -30,7 +30,7 @@ knitr::opts_chunk$set(
 
 Welcome to the `Visium_SPG_AD` project! This project involves several interactive websites, which are publicly accessible for you to browse and download.
 
-We spatially resolved transcriptomics of the inferior temporal cortex (ITC) from postmortem human brain tissue to study local gene expression profiles of brain microenvironments associated with Alzheimer’s disease (AD) related neuropathology bearing abnormal protein aggregation of amyloid beta (Abeta; Ab) and phosphorylated Tau (pTau). Using a total of 10 tissue samples from 3 donors with late-stage Alzheimer's disease (AD) and 1 age-matched control (Br3874), we generated proteomic-based, spatially-resolved transcriptome-scale (SRT) maps of the human ITC in which the immunofluorescence staining of Ab and pTau was integrated into the complementary SRT data of the identical tissue sections. With Visium Spatial Proteogenomics ([Visium-SPG](https://www.10xgenomics.com/products/spatial-proteogenomics)), we utilized a within-subjects design to study gene expression changes associated with spatially localized brain neuropathology across the 3 donors with AD (Br3854, Br3873, and Br3880). Here, using _BayesSpace_ to identify the gray-matter associated spots in a data-driven manner, we discovered statistically significant differentially expressed genes in the core (Ab spots) and peripheral (next_Ab spots) compartments of Ab-associated microenvironment in the gray matter of ITC. For more detailed information about study design and experimental results, please refer to our [manuscript](https://doi.org/10.1101/TODO). This work was performed by the [Keri Martinowich](https://www.libd.org/team/keri-martinowich-phd/), [Kristen Maynard](https://www.libd.org/team/kristen-maynard-phd/), and [Leonardo Collado-Torres](http://lcolladotor.github.io/) teams at the [Lieber Institute for Brain Development](libd.org) as well as [Stephanie Hicks](https://www.stephaniehicks.com/)'s group from [JHBSPH's Biostatistics Department](https://publichealth.jhu.edu/departments/biostatistics). This project was done in collaboration with [10x Genomics](https://www.10xgenomics.com/).
+We spatially resolved transcriptomics of the inferior temporal cortex (ITC) from postmortem human brain tissue to study local gene expression profiles of brain microenvironments associated with Alzheimer’s disease (AD) related neuropathology bearing abnormal protein aggregation of amyloid beta (Abeta; Ab) and phosphorylated Tau (pTau). Using a total of 10 tissue samples from 3 donors with late-stage Alzheimer's disease (AD) and 1 age-matched control (Br3874), we generated proteomic-based, spatially-resolved transcriptome-scale (SRT) maps of the human ITC in which the immunofluorescence staining of Ab and pTau was integrated into the complementary SRT data of the identical tissue sections. With Visium Spatial Proteogenomics ([Visium-SPG](https://www.10xgenomics.com/products/spatial-proteogenomics)), we utilized a within-subjects design to study gene expression changes associated with spatially localized brain neuropathology across the 3 donors with AD (Br3854, Br3873, and Br3880). Here, using _BayesSpace_ to identify the gray-matter associated spots in a data-driven manner, we discovered statistically significant differentially expressed genes in the core (Ab spots) and peripheral (next_Ab spots) compartments of Ab-associated microenvironment in the gray matter of ITC. For more detailed information about study design and experimental results, please refer to our [manuscript](https://doi.org/10.1101/2023.04.20.537710). This work was performed by the [Keri Martinowich](https://www.libd.org/team/keri-martinowich-phd/), [Kristen Maynard](https://www.libd.org/team/kristen-maynard-phd/), and [Leonardo Collado-Torres](http://lcolladotor.github.io/) teams at the [Lieber Institute for Brain Development](libd.org) as well as [Stephanie Hicks](https://www.stephaniehicks.com/)'s group from [JHBSPH's Biostatistics Department](https://publichealth.jhu.edu/departments/biostatistics). This project was done in collaboration with [10x Genomics](https://www.10xgenomics.com/).
 
 This project involves the [LieberInstitute/Visium_SPG_AD](https://github.com/LieberInstitute/Visium_SPG_AD) GitHub repository.
 
@@ -96,14 +96,24 @@ We value public questions, as they allow other users to learn from the answers.
 
 ## Citing our work
 
-Please cite this [manuscript](https://doi.org/10.1101/TODO) if you use data from this project.
+Please cite this [manuscript](https://doi.org/10.1101/2023.04.20.537710) if you use data from this project.
 
-> TODO
+> Influence of Alzheimer's disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex.
+> Sang Ho Kwon, Sowmya Parthiban, Madhavi Tippani, Heena R Divecha, Nicholas J Eagles, Jashandeep S Lobana, Stephen R Williams, Michelle Mark, Rahul A Bharadwaj, Joel E Kleinman, Thomas M Hyde, Stephanie C Page, Stephanie C Hicks, Keri Martinowich, Kristen R Maynard, Leonardo Collado-Torres.
+> bioRxiv 2023.04.20.537710; doi: https://doi.org/10.1101/2023.04.20.537710
 
 Below is the citation in [`BibTeX`](http://www.bibtex.org/) format.
 
 ```
-@article {TODO,
+@article {Kwon2023.04.20.537710,
+	author = {Sang Ho Kwon and Sowmya Parthiban and Madhavi Tippani and Heena R Divecha and Nicholas J Eagles and Jashandeep S Lobana and Stephen R Williams and Michelle Mark and Rahul A Bharadwaj and Joel E Kleinman and Thomas M Hyde and Stephanie C Page and Stephanie C Hicks and Keri Martinowich and Kristen R Maynard and Leonardo Collado-Torres},
+	title = {Influence of Alzheimer{\textquoteright}s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex},
+	elocation-id = {2023.04.20.537710},
+	year = {2023},
+	doi = {10.1101/2023.04.20.537710},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2023/04/20/2023.04.20.537710},
+	eprint = {https://www.biorxiv.org/content/early/2023/04/20/2023.04.20.537710.full.pdf},
 	journal = {bioRxiv}
 }
 ```

README.md

@@ -33,8 +33,8 @@ discovered statistically significant differentially expressed genes in
 the core (Ab spots) and peripheral (next_Ab spots) compartments of
 Ab-associated microenvironment in the gray matter of ITC. For more
 detailed information about study design and experimental results, please
-refer to our [manuscript](https://doi.org/10.1101/TODO). This work was
-performed by the [Keri
+refer to our [manuscript](https://doi.org/10.1101/2023.04.20.537710).
+This work was performed by the [Keri
 Martinowich](https://www.libd.org/team/keri-martinowich-phd/), [Kristen
 Maynard](https://www.libd.org/team/kristen-maynard-phd/), and [Leonardo
 Collado-Torres](http://lcolladotor.github.io/) teams at the [Lieber
@@ -172,14 +172,29 @@ work!
 
 ## Citing our work
 
-Please cite this [manuscript](https://doi.org/10.1101/TODO) if you use
-data from this project.
+Please cite this [manuscript](https://doi.org/10.1101/2023.04.20.537710)
+if you use data from this project.
 
-> TODO
+> Influence of Alzheimer’s disease related neuropathology on local
+> microenvironment gene expression in the human inferior temporal
+> cortex. Sang Ho Kwon, Sowmya Parthiban, Madhavi Tippani, Heena R
+> Divecha, Nicholas J Eagles, Jashandeep S Lobana, Stephen R Williams,
+> Michelle Mark, Rahul A Bharadwaj, Joel E Kleinman, Thomas M Hyde,
+> Stephanie C Page, Stephanie C Hicks, Keri Martinowich, Kristen R
+> Maynard, Leonardo Collado-Torres. bioRxiv 2023.04.20.537710; doi:
+> <https://doi.org/10.1101/2023.04.20.537710>
 
 Below is the citation in [`BibTeX`](http://www.bibtex.org/) format.
 
-    @article {TODO,
+    @article {Kwon2023.04.20.537710,
+        author = {Sang Ho Kwon and Sowmya Parthiban and Madhavi Tippani and Heena R Divecha and Nicholas J Eagles and Jashandeep S Lobana and Stephen R Williams and Michelle Mark and Rahul A Bharadwaj and Joel E Kleinman and Thomas M Hyde and Stephanie C Page and Stephanie C Hicks and Keri Martinowich and Kristen R Maynard and Leonardo Collado-Torres},
+        title = {Influence of Alzheimer{\textquoteright}s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex},
+        elocation-id = {2023.04.20.537710},
+        year = {2023},
+        doi = {10.1101/2023.04.20.537710},
+        publisher = {Cold Spring Harbor Laboratory},
+        URL = {https://www.biorxiv.org/content/early/2023/04/20/2023.04.20.537710},
+        eprint = {https://www.biorxiv.org/content/early/2023/04/20/2023.04.20.537710.full.pdf},
         journal = {bioRxiv}
     }