scRNASeqDB – A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells

Single-cell RNA sequencing (scRNA-Seq) is rapidly becoming a powerful tool for high-throughput transcriptomic analysis of cell states and dynamics at the single cell level. Both the number and quality of scRNA-Seq datasets have dramatically increased recently. A database that can comprehensively collect, curate, and compare expression features of scRNA-Seq data in humans has not yet been built.

Here, researchers from the University of Texas Health Science Center at Houston present scRNASeqDB, a database that includes almost all the currently available human single cell transcriptome datasets (n = 38) covering 200 human cell lines or cell types and 13,440 samples. The online web interface allows users to rank the expression profiles of the genes of interest across different cell types. It also provides tools to query and visualize data, including Gene Ontology and pathway annotations for differentially expressed genes between cell types or groups. The scRNASeqDB is a useful resource for single cell transcriptional studies.


Flowchart of data collection and database construction. GSE: accession number of series; GSM: accession number for samples; TPM: Transcripts Per Million.

Availability – This database is publicly available at

Cao Y, Zhu J, Jia P, Zhao Z. (2017) scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells. Genes 8(12), 368. [article]

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