10x Genomics Support/Loupe Browser/Analysis/

Loupe Browser Multiome ATAC + Gene Expression Tutorial

Loupe Browser 7.0 introduces an enhanced user interface (UI). Visit the navigation tutorial available on our new support website for a comprehensive understanding of these UI improvements.

This set of tutorials reviews the features and functionality unique to data generated by Cell Ranger ARC and the Multiome ATAC + Gene Expression kit and introduces techniques and patterns for analyzing linked gene expression and open chromatin regions. Basic Loupe functionality for Gene Expression or ATAC data will not be covered here. Visit Gene Expression and ATAC tutorials data to learn more about working with 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.

To use Loupe Browser, follow the Installation instructions provided on the software downloads page.

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 (433 MB).

Once the file is loaded, you can use it to tour the Multiome-specific features in Loupe Browser.

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

The key metrics include:

  • Targeted cell count - 3,000
  • Observed cell-associated barcodes from the pipeline - 2,714

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.

  • B Cells: MS4A1
  • Plasmacytoid DC: LILRA4
  • Myeloid DC: FCER1A
  • CD16 Monocytes: FCGR3A
  • CD14 Monocytes: CD14
  • Naive CD8 T Cells: CCR7+, CD8A
  • Naive CD4 T Cells: CCR7+, CD8A- Memory T Cells: CD4+, S100A4+, NKG7-
  • NK/Effector T Cells: NKG7, GNLY

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.