The provided dataset was originally published in Denyer and Ma et al. (2019).
Data were later re-processed in Denyer et al. (2025), and this version was used for the construction of the current browser version.
The cortex and endodermis developmental trajectories were described in the later work.

2. Querying Genes

The genes can be queried using the text input box on the left panel. Up to 30 comma-separated genes can be queried.
Alternatively, the user can upload a simple .txt file containing one gene per line.
The input can be provided as TAIR IDs (AT5G15290…) or using common names (SHR, SCR…). However, only TAIR IDs will be reported in the output plots.
In some cases, common names can refer to multiple unique TAIR IDs (ATM1, ARF3…). In such cases, please use TAIR IDs instead.
Please note that querying a large number of genes can lead to slow data processing.
The expression of some genes is altered during the single-cell library preparation as a cell response to the protoplasting process (protoplasting-induced genes). If the queried genes were identified as significantly affected, a warning (yellow) will be displayed in the bottom-right screen corner. Yet, querying such genes can still deliver informative results.
If the queried genes are not present in the dataset, an error notification (red) will be displayed in the bottom-right screen corner, and the gene will not appear in the output plot.

3. Feature Plot

The feature plot shows gene expression of individual cells (dots) projected on a UMAP visualization. A more intense red color means a higher normalized expression.
Each plot has an individual scale. Therefore, the expression levels of individual genes cannot be directly compared using the color intensities without considering the scale bar.
For interpretation of observed expression patterns, please refer to the cluster annotation on the left panel.

4. Expression level

The violin plots show the normalized gene expression of the cells (dots) within individual clusters.
In the case of lowly expressed genes, the violin plots can look like lines. This is an expected behavior due to many cells (dots) accumulated at zero values.
The average expression levels per cluster are reported in the ‘Average expression’ table.

5. Developmental Trajectories

The dynamics of gene expression over the tissue developmental trajectory can be explored at the ‘Trajectory Expression Plot’ and ‘Trajectory Expression Heatmap’ sections.
The individual cells of the trajectory are ordered based on pseudotime values, representing a developmental continuum.
The identities of cells in different trajectory regions and pseudotime values are indicated on the color bar on the top.
The ’Trajectory Expression Plot’ shows the expression values of individual cells and a smooth expression trend as a fitted cubic spline over the pseudotime. This plot is useful for plotting the expression dynamics of individual or a few genes.
The ‘Trajectory Expression Heatmap’ shows the smooth fitted curve in the form of a heatmap. This visualization is useful for exploring a larger number of genes

6. Data Download

Normalized cluster expression – A file containing normalized average expression values per cluster.
Raw cell x gene expression matrix – A matrix containing raw counts in a cell x gene format. This can be used for the atlas/trajectory reconstruction.
Lightweight Seurat object – a Seurat object containing normalized scaled expression values. Additionally, cell identity information and pseudotime values are stored here. It can be used for visualization purposes.

7. Citation

Primary Data Source: Denyer, T*., Ma, X*., Klesen, S., Scacchi, E., Nieselt, K., and Timmermans, M. (2019). Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing. Dev. Cell 48: 840-852.
Updated Atlas and Cortex and Endodermis Trajectories: WILL BE ADDED SOON.

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.

8. Contact

If you have any questions, please contact: marja.timmermans@zmbp.uni-tuebingen.de
If you wish to report a bug in the browser, please contact Pavel Solanský: pavel.solansky@zmbp.uni-tuebingen.de

User Manual