10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger3.0, printed on 12/22/2024

Creating Loupe Cell Browser Gene Lists

There are two ways to create gene lists that you can use to quickly find cells of interest within your data, as described in the Identifying Cell Types portion of the tutorial. The first is to use the Gene Expression sidebar to create and export a list of genes within Loupe Cell Browser.

However, you can create a gene list CSV file with a simple text editor, or Microsoft Excel. This may be useful if you have already identified a set of genes for a particular pathway or cell type, and want to quickly import those genes into Loupe Cell Browser.

The Loupe Cell Browser gene list file format is simple. Here's an example:

List,Name,Ensembl
T Cell Markers,CD3D,ENSG00000167286
B Cell Markers,CD79A,ENSG00000105369
B Cell Markers,CD79B,ENSG00000007312
Monocyte Markers,CD14,ENSG00000170458

The first line in the CSV file must be a header, and 'List' must be the first element. You can then either supply a 'Name' or 'Ensembl' column or both. The first entry in each row must be the list that the gene belongs to (e.g., "T Cell Markers"), then the gene name and/or Ensembl ID.

When importing a list, Loupe Cell Browser will attempt to match the rows against Ensembl IDs first, if specified, to avoid naming conflicts. If none of the genes in the list match the genes found in the dataset (e.g., importing a list of mouse genes to a human dataset), Loupe Cell Browser will notify you of this, and not import the list.

That's it! These lists are intended to be shared and reused; feel free to post them to the 10x Community if you see fit.