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.