Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileYanhui Hu, View ORCID ProfileSudhir Gopal Tattikota, View ORCID ProfileYifang Liu, Aram Comjean, Yue Gao, Corey Forman, Grace Kim, Jonathan Rodiger, Irene Papatheodorou, Gilberto dos Santos, View ORCID ProfileStephanie E. Mohr, View ORCID ProfileNorbert Perrimon
doi: https://doi.org/10.1101/2021.01.29.428862
Yanhui Hu
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
bDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yanhui Hu
Sudhir Gopal Tattikota
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sudhir Gopal Tattikota
Yifang Liu
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
bDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yifang Liu
Aram Comjean
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
bDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yue Gao
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
bDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Corey Forman
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Grace Kim
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jonathan Rodiger
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
bDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Irene Papatheodorou
cEuropean Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gilberto dos Santos
dThe Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stephanie E. Mohr
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
bDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Stephanie E. Mohr
Norbert Perrimon
aDepartment of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
bDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
eHoward Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Norbert Perrimon
  • For correspondence: perrimon@genetics.med.harvard.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

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, called 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 the 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. DRscDB serves as a web-based user interface that allows users to mine, utilize and compare gene expression data pertaining to scRNA-seq datasets from the published literature.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.flyrnai.org/tools/single_cell/web/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted January 31, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
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
bioRxiv 2021.01.29.428862; doi: https://doi.org/10.1101/2021.01.29.428862
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
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
bioRxiv 2021.01.29.428862; doi: https://doi.org/10.1101/2021.01.29.428862

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (2536)
  • Biochemistry (4983)
  • Bioengineering (3487)
  • Bioinformatics (15242)
  • Biophysics (6914)
  • Cancer Biology (5404)
  • Cell Biology (7756)
  • Clinical Trials (138)
  • Developmental Biology (4543)
  • Ecology (7162)
  • Epidemiology (2059)
  • Evolutionary Biology (10240)
  • Genetics (7522)
  • Genomics (9803)
  • Immunology (4869)
  • Microbiology (13250)
  • Molecular Biology (5151)
  • Neuroscience (29496)
  • Paleontology (203)
  • Pathology (838)
  • Pharmacology and Toxicology (1468)
  • Physiology (2143)
  • Plant Biology (4759)
  • Scientific Communication and Education (1013)
  • Synthetic Biology (1339)
  • Systems Biology (4015)
  • Zoology (770)