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10x Genomics
Chromium Single Cell Multiome ATAC + Gene Exp.

Loupe Browser Multiome ATAC + Gene Expression Tutorial

Welcome to the Loupe Browser Multiome ATAC + Gene Expression tutorial. The next few pages will cover the features and functionality unique to data generated by Cell Ranger ARC and the Multiome ATAC + Gene Expression kit, and introduce techniques and patterns for analyzing linked gene expression and open chromatin regions.

This tutorial will not cover basic Loupe functionality for Gene Expression or ATAC data. To get more comfortable with analyzing Gene Expression and ATAC data, visit the tutorials for those data types:

The features covered in those tutorials will also apply to Single Cell Multiome ATAC + Gene Expression datasets generated by Cell Ranger ARC.

Installing Loupe Browser

To use Loupe Browser, follow the directions on the Installation page to download and install the software on either macOS or Windows.

Download the tutorial dataset

The Multiome ATAC + Gene Expression tutorial uses a 3k human peripheral blood mononuclear cells (PBMCs) dataset that is not included with Loupe Browser. Click here to download the dataset (433MB).

Once the file is loaded, click here for a tour of Multiome-specific features.

About the Multiome ATAC + Gene Expression tutorial dataset

The tutorial dataset contains the results of a cellranger-arc run over a set of PBMCs, with the standard Chromiumâ„¢ Single Cell Multiome ATAC + Gene Expression protocol.

The key metrics include:

This dataset has been pre-annotated with cell types derived from gene expression markers. See the Annotated Cell Types category, and the Cell Type Markers gene list preloaded with the dataset.

It should be noted that T cell subtypes were more easily separable in ATAC projections, even though we used gene markers to define the subtypes.

Sharing usage data

Starting with Loupe Browser v6.1, users may choose to share anonymized non-biological usage data (i.e. no identifiable sample information such as files, cluster names, or any open text fields are tracked) to improve Loupe Browser performance. Sharing of usage data is optional, and users can change whether they want to share usage data any time. The user preference for usage data sharing will carry over within a major version (e.g. all 6.Y versions) but the user will be asked to confirm their preferences for each major version update.

In case you wish to change the usage data sharing setting, click Manage Usage Data from the Help menu and change the preference in the pop-up window.