Use of scREAD to explore and analyze single-cell and single-nucleus RNA-seq data for Alzheimer's disease

Cankun Wang; Yujia Xiang; Hongjun Fu; Qin Ma

doi:10.1016/j.xpro.2021.100513

Use of scREAD to explore and analyze single-cell and single-nucleus RNA-seq data for Alzheimer's disease

STAR Protoc. 2021 May 3;2(2):100513. doi: 10.1016/j.xpro.2021.100513. eCollection 2021 Jun 18.

Authors

Cankun Wang¹, Yujia Xiang¹, Hongjun Fu², Qin Ma¹

Affiliations

¹ Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA.
² Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA.

Abstract

Single-cell RNA-sequencing (scRNA-seq) and single-nucleus RNA-sequencing (snRNA-seq) studies have provided remarkable insights into understanding the molecular pathogenesis of Alzheimer's disease. We recently developed scREAD, a database to provide comprehensive analyses of all the existing AD scRNA-seq and snRNA-seq data from the public domain. Here, we report protocols for using the scREAD web interface and running the backend workflow locally. Our protocols enable custom analyses of AD single-cell and single-nucleus gene expression profiles. For complete details on the use and execution of this protocol, please refer to Jiang et al. (2020).

Keywords: Bioinformatics; Neuroscience; RNA-seq; Single Cell.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Alzheimer Disease* / genetics
Alzheimer Disease* / metabolism
Humans
RNA-Seq*
Single-Cell Analysis*

Abstract

Publication types

MeSH terms

Grants and funding