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  • Description: An interactive resource for users with explore our scRNA-seq developing human neocortex dataset using standard bioinformatic graphing techniques and summary statistics. Additionally, for each cell type in the developing neocortex users can explore differentially expressed genes. This tool allows users with and without programming skills to quickly obtain valuable insights and provides greater accessibility to the data itself.

    Features:• Heatmaps with gene expression across cell types in the

    developing cortex.• tSNE graphs with ability to view expression at the cell level.• Distribution graphs of gene expression for each cell type:

    Histograms or boxplots.• Summary statistics of genes across each cell type• Cell type enriched genes page: View heatmaps of enriched

    genes in each cell type, their enrichment scores and summary statistics.

    CoDEx Viewer (Cortical Development Expression Viewer)

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

  • Getting started

    • From the drop down menu choose users can choose the tool of choice.

    • The accordion menu contains descriptions for each tool .

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

  • Search bars

    • Each query tool has a search bar that allows users to enter multiple genes to be run .

    • In the top right corner the ”i” icon generates a pop up with a brief description of the tool.

    • Depending on the tool, options can be turned on and off by checkbox.

    • To select a gene begin typing the gene name, a dropdown menu will attempt to auto-complete the gene name. Press the “enter/return” key to select the gene and enter another gene.

    • To escape the dropdown menu press the “tab” key.

    • Users can copy and paste genes from a list. The genes must be unquoted and separated by a comma.

    (e.g. EOMES, SOX2, PAX6, etc..)

    • Press “Run” to generate the graph or table.

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

  • Heatmap tool

    • The heatmap tool allows users to view mean gene expression in each cell type.

    • The ”Sort genes by cell types” option sorts the genes by the level of expression in each cell type by their given ordering (“vRG”, “oRG”,…,”Mic”).

    • A schematic of layers and cell types in the developing human cortex provides user with laminae based context.

    • Cell type abbreviations are located in the bottom left table.• The graph can be downloaded using download button in the top right

    corner.

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

  • tSNE tool

    • The tSNE tool lets users view the expression of queried genes at the cell level. Users can query a single gene or multiple genes.

    • A legend is given with the cell types and their clustering via tSNEvisualization.

    • Graphs can be downloaded using the download graphs button in the top right corner.

    • The “Cell type guide” option toggles whether the clustering legend is plotted in the multi-plot.

    • The “Collective mean expression” option finds the mean of the selected genes’ expression for graphing.

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

  • Gene Distribution tool

    • The distribution tool can query the distribution of a single gene across each cell type.

    • The user can select either a boxplot of the distribution over all cell types or histograms of the distribution in each cell type.

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

  • Summary statistics

    • The summary statistic tool provides a table for statistics of genes in each cell type with: mean expression, standard deviation and the percentage of cells in which a gene is or is not expressed.

    • The user can query multiple genes (limited to 50 per query).• The table is searchable, and can be sorted (ascending/descending) by

    an of the fields in the table.

    • The table can be exported using the export table button in the top right corner.

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

  • Cell types page

    Laboratory of Daniel Geschwind, Department of Neurology, UCLA

    • The cell types page allows user to view which genes are enriched in each cell type.

    • When clicking on a cell a type a heatmap with genes sorted by enrichment score is generated for that cell type.

    • Along with the heatmap, a table with the summary statistics and enrichment scores is also generated.

    • Users can sort the table by each field as described above