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. 2017 Dec 5;8(12):368.
doi: 10.3390/genes8120368.

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

Yuan Cao  1 , Junjie Zhu  2 , Peilin Jia  3 , Zhongming Zhao  4   5   6
Affiliations

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

Yuan Cao et al. Genes (Basel). .

Abstract

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, we 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. Our 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. This database is publicly available at bioinfo.uth.edu/scrnaseqdb/.

Keywords: RNA sequencing; cell type; database; differential expression; expression profile; single cell.

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Conflict of interest statement

The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Figures

Figure 1
Figure 1
Flowchart of data collection and database construction. GSE: accession number of series; GSM: accession number for samples; TPM: Transcripts Per Million.
Figure 2
Figure 2
Gene Rank View and Gene View. (A) Gene rank list of an example gene TBK1 across all datasets; (B) Display general information of TBK1 in ‘Gene View’ page; (C) Show the gene rank of TBK1 in each cell group of GSE69405; (D) The section of gene expression displayed by heatmap and box plots. The minimum value, median value, and maximum value of the gene expression and the FDR (false discovery rate) of the gene expression comparison between groups are also displayed; (E) The top 100 positively and negatively correlated genes and annotation links are provided.
Figure 3
Figure 3
Cell View, displaying tonsil innate lymphoid cell (NK) information as an example. (A) Summary information; (B) Metadata of cell samples; (C) The top 200 upregulated genes and correlation matrices for these genes for the specific cell type or group. Note that multiple pages will be displayed when the sample or gene list is long.
Figure 4
Figure 4
Dataset View, displaying dataset GSE69405 as an example. (A) Metadata information for the dataset; (B) Cell groups and cell cluster are presented; (C) A list of differentially expressed genes between different groups is provided.
See this image and copyright information in PMC

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