This study followed the Scanpy tutorial, running clustering analysis on the 10x Genomics dataset “3k PBMCs from a Healthy Donor”.  

Explore results visually in SCP:  

• Interrogate the resulting UMAP annotated with louvain cluster numbers (follow the link or click on the “Explore” tab above)
  • evaluate whether sample-specific features might drive clustering results (change the annotation to biosample_id)
  • examine the distribution of mitochondrial gene expression across the dataset (change the annotation to percent_mito)

• Examine CST3 expression (follow the link or enter CST3 in the gene search bar and click the search icon)
• Look at CST3 gene expression in the different louvain clusters as a violin plot (after gene search, click the Distribution tab)
• Ask how a set of genes are expressed across the louvain clusters by viewing a dot plot (perform a multi-gene search for CST3 LTB IL32)
• or view per-cell gene expression in a heatmap (after multi-gene search, click the Heatmap tab)

With an SCP account (click Sign In in the upper right hand corner of the portal), you can download data from the study.  

Want to share your single cell data using SCP? Upload your data and become an SCP study owner!  

Questions? Contact us at scp-support@broadinstitute.zendesk.com.