期刊
PLANT COMMUNICATIONS
卷 3, 期 4, 页码 -出版社
ELSEVIER
DOI: 10.1016/j.xplc.2022.100302
关键词
single cell; RNA sequencing; visualization; discovery; comparison
资金
- Australian Research Council [DP210103258]
- Australian Research Council Industrial Transformation Research Hub in Medicinal Agriculture [IT180100006]
scCloudMine is a cloud-based application that allows researchers to visualize, compare, and explore single-cell transcriptome data. It provides a user-friendly platform for uploading and visualizing datasets, enabling comparative analysis of cell types and gene expression. The tool has revealed study-specific gene expression patterns and highlighted the cell-type specificity of hormone-responsive genes.
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 preprocessing 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.
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