Average Expression per Cluster






Normalized cluster expression - dusk.cluster-expression-norm.txt
Raw cell x gene expression matrix - dusk.expression-matrix-raw.txt.gz
Lightweight Seurat object - dusk.RDS
Wolffia-Arabidopsis-Maize orthologs - wolffia-arabidopsis-maize-orthologs.tsv




Average Expression per Cluster






Normalized cluster expression - dawn.cluster-expression-norm.txt
Raw cell x gene expression matrix - dawn.expression-matrix-raw.txt.gz
Lightweight Seurat object - dawn.RDS
Wolffia-Arabidopsis-Maize orthologs - wolffia-arabidopsis-maize-orthologs.tsv




Average Expression per Cluster






Normalized cluster expression - merged.cluster-expression-norm.txt
Raw cell x gene expression matrix - merged.expression-matrix-raw.txt.gz
Lightweight Seurat object - merged.RDS
Wolffia-Arabidopsis-Maize orthologs - wolffia-arabidopsis-maize-orthologs.tsv

User Manual


1. Provided Datasets

  • The provided dataset was originally published in Denyer et al. (2024).
  • The browser includes ‘Dusk’ and ‘Down’ datasets that differ in the light conditions during the sample collection. Additionally, the ‘Merged’ dataset contains both previous datasets in a single object. Individual datasets can be selected for browsing from the top panel.
  • Please see the publication for further details about the data.



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.
  • Please note that querying a large number of genes can lead to slow data processing.
  • The genes can be queried as Wolffia IDs (Wa8730a014g002860, Wa8730a010g004730…) or TAIR IDs (AT5G15290, AT3G14770…).
  • Often, Wolffia genes are linked to multiple Arabidopsis orthologs. The queried and successfully plotted genes together with the corresponding TAIR IDs will be reported on a table above the plot.
  • If the TAIR IDs are queried and a single TAIR ID is linked to multiple Wolffia orthologs, it will not be plotted but will be reported on a table below the ‘Submit’ button. The user can then specify the exact Wolffia ID(s).
  • The full Wolffia-Arabidopsis ortholog list can be obtained from the ‘Data Download’ section.



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.



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



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

  • Timmermans Lab