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bioRxiv · 10.1101/2021.05.28.446161

rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database

Osorio, D.·Kuijjer, M. L.·Cai, J. J.
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Abstract

MotivationCharacterizing cells with rare molecular phenotypes is one of the promises of high throughput single-cell RNA sequencing (scRNA-seq) techniques. However, collecting enough cells with the desired molecular phenotype in a single experiment is challenging, requiring several samples preprocessing steps to filter and collect the desired cells experimentally before sequencing. Data integration of multiple public single-cell experiments stands as a solution for this problem, allowing the collection of enough cells exhibiting the desired molecular signatures. By increasing the sample size of the desired cell type, this approach enables a robust cell type transcriptome characterization. ResultsHere, we introduce rPanglaoDB, an R package to download and merge the uniformly processed and annotated scRNA-seq data provided by the PanglaoDB database. To show the potential of rPanglaoDB for collecting rare cell types by integrating multiple public datasets, we present a biological application collecting and characterizing a set of 157 fibrocytes. Fibrocytes are a rare monocyte-derived cell type, that exhibits both the inflammatory features of macrophages and the tissue remodeling properties of fibroblasts. This constitutes the first fibrocytes unbiased transcriptome profile report. We compared the transcriptomic profile of the fibrocytes against the fibroblasts collected from the same tissue samples and confirm their associated relationship with healing processes in tissue damage and infection through the activation of the prostaglandin biosynthesis and regulation pathway. Availability and ImplementationrPanglaoDB is implemented as an R package available through the CRAN repositories https://CRAN.R-project.org/package=rPanglaoDB. Contactdaniecos@uio.no Supplementary informationCode to replicate the case example and figure 1 is available at https://github.com/dosorio/rPanglaoDB O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/446161v1_fig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@b4e67forg.highwire.dtl.DTLVardef@88a46aorg.highwire.dtl.DTLVardef@e25681org.highwire.dtl.DTLVardef@19d5bb7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Characterization of the fibrocytes transcriptome. (A) Identification of cells expressing marker genes that differentiate fibrocytes identity from macrophages and fibroblasts (CD34, ACTA2, FN1, Collagen V, FAP and SIRPA). (B) Cross validation of the identified cells expressing CD34+, ACTA2+, COL5A1+, COL5A2+, COL5A3+, FN1+, FAP+, SIRPA+, PTPRC+, MME+, and SEMA7A+ by kernel density estimation through the Nebulosa package. (C) Volcano plot displaying the differential expression between fibrocytes and the fibroblasts collected in the same merged samples. (D) Enrichment of the prostaglandin biosynthesis and regulation pathway using GSEA through the fgsea package. (E) Enrichment of the prostaglandin biosynthesis and regulation pathway using ssGSEA through the GSVA package. C_FIG

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Osorio, D., Kuijjer, M. L., Cai, J. J.. 2021-05-28. rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. https://doi.org/10.1101/2021.05.28.446161

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