Researchers at The Ohio State University have developed an integrated database known as scREAD – single-cell RNA-Seq database for Alzheimer’s Disease.
Alzheimer’s disease (AD) is the most common cause of dementia. Research estimates that currently 5.8 million Americans aged 65 and older suffer from AD. Despite years of research, there are still no effective therapies available that can cure or alter disease progress. In addition, the molecular mechanisms underlying AD are still poorly understood.
Newer techniques, including single-cell RNA sequencing (scRNA-Seq), have provided an alternative method to understanding the cellular heterogeneity of the brain and the complex changes during AD. The scRNA-Seq analysis can reveal the complex and rare cell populations, reveal regulatory relationships between genes and also track cell lineages. Understanding AD pathology at this unique cellular level has significantly improved researchers’ ability to understand AD pathogenesis.
In this paper, researchers discuss the development of their novel database called scREAD. The team designed this database to manage all existing scRNA-Seq and single-nucleus RNA-sequencing (snRNA-Seq) datasets.
Features of scREAD:
- It is the first database to contain all the 12 existing scRNA-Seq and snRNA-Seq datasets from human post-mortem brain tissue with AD and mouse models with AD pathology.
- The database redefines these 12 datasets into 55 datasets corresponding to species, gender, brain region, disease or control and age stage.
- It provides comprehensive analysis results for all 55 datasets.
- All of the analysis results are visualised through a user-friendly interface.
- All of the analyses are freely accessible as stand-alone one-line command scripts in R.
Functions of scREAD:
- It enables construction of control atlas for different brain regions in humans and mice.
- The database identifies human and mouse disease cell types based on the control atlas and subclusters.
- It pinpoints the differentially expressed genes for each cell type.
- It identifies cell-type-specific regulons.
The team believe that this freely available database will benefit AD researchers. They hope to collect more AD scRNA-Seq and snRNA-Seq from more brain regions to build up this database. They also hope to expand the database by integrating other omic data to enable more functional interpretation.
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