The Plant Single Cell Browser

About this Browser

High-throughput single-cell omics methods provide unprecedented power in understanding the complexity of plant tissues and organs. The incomparable resolution of data that single-cell RNA-sequencing (scRNA-seq) affords means that this technology is swiftly becoming a standard for transcriptomic sequencing in plants. Further, single-cell chromatin accessibility profiling (scATAC-seq) allows for investigating the epigenetic regulation underlying various processes in plant development, immunity response, and other phenomena.

This portal presents a user-friendly interface to query such data derived from plant tissues. With our recent Arabidopsis root, Arabidopsis leaf, and Wolffia australiana scRNA-Seq, detailed expression information for individual genes or gene lists can be examined.

The core and most commonly used functionality is the visualization of gene expression patterns using a ‘Feature plot’, which shows the expression levels for individual cells projected on the UMAP plot. The gene expression can be examined on a cell cluster level and visualized using a ‘Violin plot’ or a table with mean expression per cell in a cluster.

The ‘Arabidopsis Root’ datasets additionally provide an option to explore dynamics of gene expression over the developmental trajectories, which is explained in the ‘User Manual’.

Tips on how to derive the detailed spatiotemporal expression information uniquely captured by the data, as well as details on specific datasets, can be found in the ‘User Manual’.

Please select the dataset of interest listed on the top of this page to enter the data browser.

We offer an opportunity to host other single-cell datasets. If you are interested in the construction of a similar online browser using your data, please do not hesitate to contact Marja Timmermans.

If you make use of the data presented here, please cite the following article in addition to the primary data sources:

Ma, X., Denyer, T., & Timmermans, M. (2020). PscB: A Browser to Explore Plant Single Cell RNA-Sequencing Data Sets. Plant physiology, 183(2), 464–467.

Primary Data Sources

Arabidopsis Root scRNA-seq

Denyer, T., Ma, X., Klesen, S., Scacchi, E., Nieselt, K., & Timmermans, M. (2019). Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing. Developmental cell, 48(6), 840–852.e5.

Arabidopsis Root scATAC-seq

Coming soon

Arabidopsis Leaf scRNA-seq

Kim, J. Y., Symeonidi, E., Pang, T. Y., Denyer, T., Weidauer, D., Bezrutczyk, M., Miras, M., Zöllner, N., Hartwig, T., Wudick, M. M., Lercher, M., Chen, L. Q., Timmermans, M., & Frommer, W. B. (2021). Distinct identities of leaf phloem cells revealed by single cell transcriptomics. The Plant cell, 33(3), 511–530.

Wolffia australiana scRNA-seq

Denyer, T., Wu, P. J., Colt, K., Abramson, B. W., Pang, Z., Solansky, P., Mamerto, A., Nobori, T., Ecker, J. R., Lam, E., Michael, T. P., & Timmermans, M. C. P. (2024). Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana. Genome research, 34(7), 1106–1120. https://doi.org/10.1101/gr.279091.124

Acknowledgments

We thank Dieter Steinmetz and Andreas Keck for installation and maintenance of the server.

Funding was provided by the Alexander von Humboldt Foundation.