10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger2.0, printed on 12/22/2024

Loupe Cell Browser Gene Expression Tutorial

Welcome to the Loupe Cell Browser gene expression tutorial. In the next few pages, we will be finding significant genes, identifying functional cell types, and exploring substructure within a real-world dataset. Along the way, we'll touch on most of the features of Loupe Cell Browser.

Setup

Before beginning the tutorial, make sure you have downloaded Loupe Cell Browser. If this is your first time working with Loupe Cell Browser, you can access the AMLTutorial dataset by clicking on the AMLTutorial link on the Recent Files page:

You can also access the tutorial dataset by clicking on 'Load Tutorial' from the Help menu. Once you've loaded the AMLTutorial file, click here to tour the user interface.

About the AMLTutorial Dataset

The AMLTutorial dataset contains the results of a cellranger aggr run over three samples: two healthy control samples of frozen human bone marrow mononuclear cells, and a pre-transplant sample from a patient with acute myeloid leukemia (AML). This dataset was generated in collaboration with the Fred Hutchinson Cancer Research Center, and referenced in the Nature Communications publication, "Zheng et al, Massively parallel digital transcriptional profiling of single cells" (2017; doi:10.1038/ncomms14049).