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index.Rmd
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---
title: scRNA-seq of human vitiligo reveals complex networks of subclinical immune
activation and a role for CCR5 in Treg function
---
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This site provides access to the data we used in our recent publication ([Gellatly et. al 2021](https://www.science.org/doi/10.1126/scitranslmed.abd8995)) where we sought to identify cellular communications that show disruption in lesions or in non-lesional skins of individuals suffering from Vitiligo, an autoimmune skin disease characterized by the targeted destruction of melanocytes by T cells.
The data provided was obtained using our in-house [inDrop system](https://dx.doi.org/10.1016%2Fj.cell.2015.04.044) to generate single cell RNA-Seq profiles on affected and unaffected skin from vitiligo patients, as well as healthy controls. The data was analyzed using our end-to-end scRNA data analysis package called [SignallingSingleCell](./signallingsinglecell.html).
To provide access to the processed data we are hosting an interactive browser based on [Cellxgene](./browse.html) Browser.
All raw sequencing data was processed by the scRNA-Seq inDrop pipeline developed within the interactive pipeline manager [DolphinNext](./dolphinnext.html) ([Yukselen et. al 2020](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6714-x)), and currently being hosted in DolphinSuite high throughput data analysis platform.
##### **Raw Data:**
The raw .fastq files have been deposited through dbGAP. These files are protected, and you will need an account and to request access to download the files. As of 10/5/21 the data files are processing on the dbGAP server.
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002455.v1.p1
##### **UMI Tables:**
For convenience we are providing 3 processed data tables here. One is a raw sparse matrix, that is the output of our processing pipeline with no further manipulation. We are also providing a fully processed UMI table that has been filtered, dimension reduced, clustered, and normalized. The processed UMI table is provided in the <a href="https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf" target="_blank">ExpressionSet</a> class format. We are also providing a separate processed UMI table for the T Cells.
<a href="https://vitiligo.dolphinnext.com/data/phs002455.v1.p1_UMITable.Rdata" target="_blank">Raw UMI Table</a>
<a href="https://vitiligo.dolphinnext.com/data/phs002455_processed_UMItable.Rdata" target="_blank">Processed UMI Table</a>
<a href="https://vitiligo.dolphinnext.com/data/phs002455_TCells_processed_UMItable.Rdata" target="_blank">Processed UMI Table of T-cells</a>
<img width="70%" height="70%" src="./images/networkanalysis.png" class="center">