Cell Exploration

From the Repertoire Metadata Search page (also accessible via the top navigation menu), click on the Cell Search Results tab. The updated green colour scheme confirms you have accessed the cell workflow and are viewing metadata for cell samples. In this context, “cell” specifies a reference point for all data that can be related to an individual cell, providing a mechanism to link e.g. gene and protein expression (from single-cell transcriptome sequencing or flow cytometry) and paired chains for rearrangements (e.g. heavy/light, alpha/beta). Such data can be obtained from the 10x immune profiling platform. For information on creating Cell and Expression files from 10x data, see here

As with sequence/clone metadata, from this page you can apply filters, customize the displayed metadata, and download metadata. Click the Browse Cells button to enter stage 2 of the search.

This opens a new Cell Search page, analogous to the Sequence and Clone Search pages. Here you can apply cell-level filters, customize the displayed annotation fields, and download all cell-linked data (in this example, linked gene expression and rearrangements for B and T cells). An overview of each cell is shown, with Chain 1 and Chain 2 indicating the paired rearrangements for a specific cell (defined by Cell Index), and Properties listing the top four highest expressed genes (Ensembl nomenclature). Note that Tool Cell Index is not guaranteed to be unique outside the data processing for a single repertoire while Cell Index is unique within the repository.

If you are interested in a specific marker gene, you can filter cells based on minimum expression of this gene, as shown here for CD4. To filter on multiple genes, you will need to use the ADC API.

Scrolling down to the bottom of the page, you can see the available Analysis Apps for cell data. Conga detects correlation between T cell gene expression profile and TCR sequences  in single-cell datasets, and CellTypist is an automated cell type annotation tool. See the Analysis Page for more information on running jobs.