• WHAT: Single Cell RNA-Seq
  • WHEN: June 17th, 10am-12pm & 1-3:30pm
  • WHERE: Online; instructions upon registration
  • WHO: Ansuman Chattopahyay & Sri Chaparala
  • HOW: Register here


This is a 4½ 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 – 3:30 pm) focuses on software demonstration using HSLS-licensed Partek Flow software.

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

Hands-On Follow Up:

Every Wednesday after a workshop, a follow up session (1 pm – 3 pm) will review the hands-on exercise questions distributed during the workshop. We will not be addressing questions on data analysis for personal research projects—researchers are encouraged to request a one-on-one consultation with MBIS for this type of discussion. Registration is not required for the hands-on follow up session. To attend, use the same Zoom link you receive upon registration for this workshop.

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 Requirements:

Workshop Guide:

Suggested Reading:

Attribution:

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.

HSLS Summer 2020 MolBio Info Service Training Workshops schedule

Contact the HSLS Molecular Biology Information Service with any questions.

(Photo by National Cancer Institute on Unsplash)