Single Cell RNA-Seq

Workshop Objective:

This is a 5 hour workshop on the techniques, platforms, and methods used in analyzing single cell RNA-Seq data (scRNA-Seq). The morning session (10 am - 12 pm) starts with a presentation from the Genomics Research Core on best practices in sample handling, followed by an overview of the basic steps involved in scRNA-Seq data analysis. The afternoon session (1 pm - 4 pm) focuses on software demonstration using HSLS-licensed Partek Flow software.

One week after this class we will host a follow up session (1 pm to 3 pm) to review the hands-on exercise questions distributed during the workshop. Registration is not required for the hands-on follow up session. To attend, use the same Zoom link you received upon registration for the original workshop.   

Participants will learn how to

  • import FASTQ files from scRNA-Seq experiments using GEO
  • perform quality checks (QC) on single cell data
  • filter and normalize of data
  • generate PCA and t-SNE plots to visualize data
  • identify cell populations, biomarkers, and differential gene expression
  • perform trajectory analyses

Target Audience:

Experimental biologists seeking to analyze scRNA-Seq data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.

Workshop Guide:

Suggested Reading:


Please include the following statement in the acknowledgments section for all publications, posters, and presentations: Data analysis was performed using {name of software} software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.

Class Type

Upcoming Classes

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