Dendrogram

This tab displays the mean expression of up to 20 genes over each cluster in the mouse single-cell RNA-seq developmental atlas.

• Clusters are ordered according to the dendrogram which represents a molecular taxonomy of all cell populations

• Below the dendrogram, clusters are annotated by brain region, time point, and a cell cycle G2/M phase score

• Bubble colour encodes the mean expression within the cluster, and bubble size encodes the proportion of cells within each cluster that express the gene

• Hover over each bubble, or move to the tab containing the table, to get additional details about each cluster & its expression level

• When selecting more than one gene, use the sidebar switch to plot the mean expression over these genes in a new row of the bubble plot. Note that Pct values are disregarded here, so all bubbles in this row are the same size

Cluster information

Gene detection rate by cluster

This table compares the detection rate of up to 20 genes in each cluster from the mouse single-cell RNA-seq development atlas.

• Sidebar gene input is optional for this tab. Cluster information and the marker table will display before any genes have been entered.

• When genes are entered in the sidebar, the value in each gene's column denotes the detection rate of the gene in cells of the specified cluster

• Use the button(s) below the table to download TSV files of the table contents. Click "Download cluster information table" for the cluster information only. A second button named "Download detection rate table" will display when a gene is entered into the app. This button provides a TSV file containing the mean expression of each input gene in each cluster, as well as a percentage of cells in each cluster expressing the gene

• Select a cluster using the radio button to the left of each row to view the cluster's gene markers below (sidebar update button not required)

• Search the table's contents using the search box to the top right of the table

• Click on the column headers to sort the table by ascending and descending values, and click and drag the column dividers in the header row to resize the columns

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Cluster markers

This table displays the 100-gene signature for the cluster selected in the expression table above.

• The signature comprises the 100 genes with the lowest adjusted p-value (highest significance) in the cluster

• Detection rates are calculated as the proportion of cells in the specified population expressing the gene

• Specificity is calculated as the difference between the detection rate within the cluster and outside of the cluster

• Search the table's contents using the search box to the top right of the table

• Click on the column headers to sort the table by ascending and descending values, and click and drag the column dividers in the header row to resize the columns

Timecourse

This plot quantifies the proportion of cells (from 0 to 1) at each timepoint where a given gene is detected, broken down by cell type, to allow for visualizing expression across the timecourse.

• Use the side bar to select which brain region to interrogate

• Use the switch above the plot to toggle between static and interactive plots (sidebar update button not required)

• As only one gene can be plotted at a time, use the dropdown tool above the plots to choose which of the input genes to display (sidebar update button not required)

• Download the static version of the plot as a pdf using the button below the plot

• Be aware of the y-axis, which is computed as the max for each gene

Single-cell expression, by region

Use this tab to explore the expression of one or more genes at the single-cell level per brain region.

• In the top row, the cells are plot in 2D according to a dimensionality reduction algorithm, coloured by cluster (left) or expression (right)

• If using tSNE or UMAP reduction, hover over the plot coloured by cluster (top left) to identify each cluster. Hover will be disabled if clusters are labeled

• In the bottom row, violin plots display expression in each cluster, ordered by mean expression

• If more than one gene is provided, the mean expression of all genes is automatically computed and displayed

Single-cell expression, by sample

Use these tabs to explore the expression of one or more genes at the single-cell level in each sample.

• In the top row of tSNE plots, the cells are plot in the 2D tSNE space and coloured by cluster. In the bottom row, they are instead coloured by expression

• Each violin plot is coloured by cluster and ordered by the expression level within the given sample

• If more than one gene is provided, the mean expression of all genes is automatically computed and displayed in both tabs

Clusters ranked by expression

This plot displays the mean expression of the selected gene in each cluster, ranked from highest to lowest expression.

• The ticks below the plot x-axis provide a general categorization by cell type

• Use the dropdown tool above the plot to choose which of the input genes to display (sidebar update button not required), or use the sidebar toggle to display mean expression over all input genes (sidebar update button required)

• Be aware of the y-axis, which is bounded by the maximum expression value present

• Use the horizontal scroll bar at the bottom of the plot to view the plot's full width

• Download the plot as a PDF file using the button below the plot

Cell types clustered by expression

This plot is a heatmap clustering input genes and cell types together based on their mean expression within clusters.

• The heatmap's hierarchical clustering method requires at least two genes as input. An error message will display if only one gene is provided

• At least one cell type must be selected: an error message will display if none are checked off

• The coloured bar above the heatmap provides a categorization of cell clusters by general cell type

• The tree to the left of the heatmap indicates the clustering of genes, and the tree above the heatmap indicates the clustering of cell types

• Download the plot as a PDF file using the button below the plot