DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species

Yanhui Hu; Sudhir Gopal Tattikota; Yifang Liu; Aram Comjean; Yue Gao; Corey Forman; Grace Kim; Jonathan Rodiger; Irene Papatheodorou; Gilberto Dos Santos; Stephanie E Mohr; Norbert Perrimon

doi:10.1016/j.csbj.2021.04.021

DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species

Comput Struct Biotechnol J. 2021 Apr 11:19:2018-2026. doi: 10.1016/j.csbj.2021.04.021. eCollection 2021.

Authors

Yanhui Hu^{1

2}, Sudhir Gopal Tattikota¹, Yifang Liu^{1

2}, Aram Comjean^{1

2}, Yue Gao^{1

2}, Corey Forman¹, Grace Kim¹, Jonathan Rodiger^{1

2}, Irene Papatheodorou³, Gilberto Dos Santos⁴, Stephanie E Mohr^{1

2}, Norbert Perrimon^{1

2

5}

Affiliations

¹ Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
² Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
³ European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
⁴ The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
⁵ Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

Abstract

With the advent of single-cell RNA sequencing (scRNA-seq) technologies, there has been a spike in studies involving scRNA-seq of several tissues across diverse species including Drosophila. Although a few databases exist for users to query genes of interest within the scRNA-seq studies, search tools that enable users to find orthologous genes and their cell type-specific expression patterns across species are limited. Here, we built a new search database, DRscDB (https://www.flyrnai.org/tools/single_cell/web/), to address this need. DRscDB serves as a comprehensive repository for published scRNA-seq datasets for Drosophila and relevant datasets from human and other model organisms. DRscDB is based on manual curation of Drosophila scRNA-seq studies of various tissue types and their corresponding analogous tissues in vertebrates including zebrafish, mouse, and human. Of note, our search database provides most of the literature-derived marker genes, thus preserving the original analysis of the published scRNA-seq datasets. Finally, DRscDB serves as a web-based user interface that allows users to mine gene expression data from scRNA-seq studies and perform cell cluster enrichment analyses pertaining to various scRNA-seq studies, both within and across species.

Keywords: Cross-species analysis; Data mining; Model organisms; single-cell RNA-seq.

Abstract

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