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Welcome to Barvista, an online visualization of gene expression in barley meristem cells. Displayed here is data from Hordeum vulgare with the genome assembly HORVU.MOREX.r3

. It consists of three scRNAseq datasets, Rep1, Rep2 and Rep3, as well as one spatial dataset from molecular cartography, MC. By combining the information gained from both datasets, gene expression for 48,904 barley genes were predicted and linked to specific cells within the tissue.

This site offers two different views of the data. On the left side is the interaction menu and the clustered data displayed in an UMAP plot. On the right side is the visualization of different clusters within the tissue of the barley inflorescence. At the bottom the gene expression of the individual clusters is displayed.

Image interactions: Both images can be zoomed in and out of using the zoom buttons. Clicking the reset button or clicking once inside either image will reset the zoom to default. The tissue plot on the right can be either dragged using the drag button. A subset of cells from the tissue plot can be selected using the selection button.

Select dataset

Select one of the datasets from the dropdown list.

Input gene name

Add a valid gene ID to visualize the expression in the tissue and the UMAP plot, e.g. 4GH0396400.

Gene(s) not available

Reset visualization

Reset cluster highlights and gene expression values.

Cluster selection

Highlight a specific cluster.

Show mouse hover infobox

Enable/disable the infobox display when hovering over cells with the mouse.

The bottom table displays information about gene expression depending on the cluster. It is derived from the measured data from the sc-RNAseq samples rep1, rep2 and rep3, not from the imputed Molecular Cartography data. The data is pre-filtered by pct.1 and pct.2, to ensure that each gene was expressed in at least 1% of cells within the displayed cluster or within all other clusters. The pre-filtering can be disabled using the checkbox above the table.

Show data for cluster:
Allow pre-filtering by pct: