ScCloudMine: A cloud-based app for visualization, comparison, and exploration of single-cell transcriptomic data

Abstract

scCloudMine is a cloud-based application for visualization, comparison, and exploration of single-cell transcriptome data. It does not require an on-site, high-power computing server, installation, or associated expertise and expense. Users upload their own or publicly available scRNA-seq datasets after pre-processing for visualization using a web browser. The data can be viewed in two color modes—Cluster, representing cell identity, and Values, showing levels of expression—and data can be queried using keywords or gene identification number(s). Using the app to compare studies, we determined that some genes frequently used as cell-type markers are in fact study specific. The apparent cell-specific expression of PHO1;H3 differed between GFP-tagging and scRNA-seq studies. Some phosphate transporter genes were induced by protoplasting, but they retained cell specificity, suggesting that cell-specific responses to stress (i.e., protoplasting) can occur. Examination of the cell specificity of hormone response genes revealed that 132 hormone-responsive genes display restricted expression and that the jasmonate response gene TIFY8 is expressed in endodermal cells, in contrast to previous reports. It also appears that JAZ repressors have cell-type-specific functions. These features identified using scCloudMine highlight the need for resources to enable biological researchers to compare their datasets of interest under a variety of parameters. scCloudMine enables researchers to form new hypotheses and perform comparative studies and allows for the easy re-use of data from this emerging technology by a wide variety of users who may not have access or funding for high-performance on-site computing and support.