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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</title>
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<h1 class="title toc-ignore">scRNA-seq of human vitiligo reveals complex networks of subclinical immune activation and a role for CCR5 in Treg function</h1>
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<p>This site provides access to the data we used in our recent publication (<a href="https://www.science.org/doi/10.1126/scitranslmed.abd8995">Gellatly et. al 2021</a>) 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.</p>
<p>The data provided was obtained using our in-house <a href="https://dx.doi.org/10.1016%2Fj.cell.2015.04.044">inDrop system</a> 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 <a href="./signallingsinglecell.html">SignallingSingleCell</a>.</p>
<p>To provide access to the processed data we are hosting an interactive browser based on <a href="./browse.html">Cellxgene</a> Browser.</p>
<p>All raw sequencing data was processed by the scRNA-Seq inDrop pipeline developed within the interactive pipeline manager <a href="./dolphinnext.html">DolphinNext</a> (<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6714-x">Yukselen et. al 2020</a>), and currently being hosted in DolphinSuite high throughput data analysis platform.</p>
<div id="raw-data" class="section level5">
<h5><strong>Raw Data:</strong></h5>
<p>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.</p>
<p><a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002455.v1.p1" class="uri">https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002455.v1.p1</a></p>
</div>
<div id="umi-tables" class="section level5">
<h5><strong>UMI Tables:</strong></h5>
<p>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.</p>
<p><a href="https://vitiligo.dolphinnext.com/data/phs002455.v1.p1_UMITable.Rdata" target="_blank">Raw UMI Table</a></p>
<p><a href="https://vitiligo.dolphinnext.com/data/phs002455_processed_UMItable.Rdata" target="_blank">Processed UMI Table</a></p>
<p><a href="https://vitiligo.dolphinnext.com/data/phs002455_TCells_processed_UMItable.Rdata" target="_blank">Processed UMI Table of T-cells</a></p>
<p><img width="70%" height="70%" src="images/networkanalysis.png" class="center"></p>
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