A single-cell molecular map of mouse gastrulation and early organogenesis.
This is the accompanying interactive server for the paper A single-cell molecular map of mouse gastrulation and early organogenesis.
Please note: when you reach this page, the server needs to load some data for your session. We have noticed this is particularly slow on Google Chrome, so please be patient!
Tabs:
Dataset overview: Reduced dimension plots of the data are shown with customisable colouring, with a visualisation of how cells from different timepoints contribute to different cell populations.Gene interrogation: The patterns of expression of genes across the dataset may be viewed here.
Cell-type markers: Genes highly expressed in a single celltype are shown here.
Endoderm: Interactive versions of plots from Figure 2 of the manuscript are shown - these will change depending on your gene selection.
Haematoendothelium: Customisable versions of the force-directed graph from Figure 3 of the manuscript are shown - these will change depending on your gene selection.
Options:
Projection type: Select the type of visualisation you want.Cell subset: Select the timepoints you want to plot.
Plot colour: Select the variable you would like to colour the overview plots by. The options Timepoint cluster and Theiler cluster are only appropriate when visualising a single timepoint or Theiler stage respectively.
Gene: Select the gene (MGI) to use for expression plots.
Annotate clusters: Text will be drawn on the plot to help locate specific cell types.
Subset cells & severity: To speed up plotting, this reduces the number of cells plotted in a density dependent manner.
Other notes:
To report any issues please contact Jonny Griffiths at jag216 {at} cam.ac.uk, or John Marioni at marioni {at} ebi.ac.uk.It takes a few seconds to make the first plots when all cells are considered - this should speed up when parameters are changed thereafter.
You can download the processed data using the script at our Github repo.