CellDepot: A Unified Repository for scRNA-seq Data and Visual Exploration

Dongdong Lin; Yirui Chen; Soumya Negi; Derrick Cheng; Zhengyu Ouyang; David Sexton; Kejie Li; Baohong Zhang

doi:10.1016/j.jmb.2021.167425

CellDepot: A Unified Repository for scRNA-seq Data and Visual Exploration

J Mol Biol. 2022 Jun 15;434(11):167425. doi: 10.1016/j.jmb.2021.167425. Epub 2021 Dec 28.

Authors

Dongdong Lin¹, Yirui Chen², Soumya Negi³, Derrick Cheng⁴, Zhengyu Ouyang⁵, David Sexton⁶, Kejie Li⁷, Baohong Zhang⁸

Affiliations

¹ Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA. Electronic address: dongdong.lin@biogen.com.
² Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA. Electronic address: yirui.chen@biogen.com.
³ Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA. Electronic address: soumya.negi@biogen.com.
⁴ BioInfoRx, Inc., 510 Charmany Dr, Suite 275A, Madison, WI 53719, USA. Electronic address: derrick@bioinforx.com.
⁵ BioInfoRx, Inc., 510 Charmany Dr, Suite 275A, Madison, WI 53719, USA. Electronic address: oyoung@bioinforx.com.
⁶ Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA. Electronic address: david.sexton@biogen.com.
⁷ Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA. Electronic address: kejie.li@biogen.com.
⁸ Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA. Electronic address: baohong.zhang@biogen.com.

PMID: 34971674
DOI: 10.1016/j.jmb.2021.167425

Abstract

CellDepot containing over 270 datasets from 8 species and many tissues serves as an integrated web application to empower scientists in exploring single-cell RNA-seq (scRNA-seq) datasets and comparing the datasets among various studies through a user-friendly interface with advanced visualization and analytical capabilities. To begin with, it provides an efficient data management system that users can upload single cell datasets and query the database by multiple attributes such as species and cell types. In addition, the graphical multi-logic, multi-condition query builder and convenient filtering tool backed by MySQL database system, allows users to quickly find the datasets of interest and compare the expression of gene(s) across these. Moreover, by embedding the cellxgene VIP tool, CellDepot enables fast exploration of individual dataset in the manner of interactivity and scalability to gain more refined insights such as cell composition, gene expression profiles, and differentially expressed genes among cell types by leveraging more than 20 frequently applied plotting functions and high-level analysis methods in single cell research. In summary, the web portal available at http://celldepot.bxgenomics.com, prompts large scale single cell data sharing, facilitates meta-analysis and visualization, and encourages scientists to contribute to the single-cell community in a tractable and collaborative way. Finally, CellDepot is released as open-source software under MIT license to motivate crowd contribution, broad adoption, and local deployment for private datasets.

Keywords: cellxgene; data visualization; scRNA-seq portal; single cell; single-cell RNAseq.

MeSH terms

Datasets as Topic*
Exome Sequencing
Gene Expression Profiling
Internet Use*
RNA-Seq*
Single-Cell Analysis*
Software*
Transcriptome*