This is a 5 hour workshop. The morning session (10 am - 12 pm) starts with a presentation from the Genomics Research Core on best practices in sample handling, followed by a brief introduction to techniques, platforms, and methods used in bulk RNA-Seq experiments.  The afternoon session (1 pm - 4 pm) focuses on software demonstration using the HSLS-licensed CLC Genomics Workbench.

Registration is required. Please register here.

Class Details:

Participants will learn how to

• access the CLCbio Genomics Server hosted on the HTC Cluster by Pitt CRC
• import RNA-Seq FASTQ reads from a GEO dataset
• assess the quality of RNA-Seq data
• align reads to a reference genome
• estimate known gene and transcript expression
• perform differential expression analysis
• visualize data by generating PCA and heatmaps

Target Audience:

Experimental biologists seeking to analyze bulk RNA-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:

Register for CLC Genomics Workbench

Workshop Guide:

https://hsls.libguides.com/MolBioWorkshops/BulkRNAseqCLC

Suggested Reading:

• Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., … Mortazavi, A. (2016). A survey of best practices for RNA-seq data analysis. Genome Biology, 17(1), 13. doi:10.1186/s13059-016-0881-8
• Pulikkan, J. A., Hegde, M., Ahmad, H. M., Belaghzal, H., Illendula, A., Yu, J., … Castilla, L. H. (2018). CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell, 174(1), 172–186.e21. doi:10.1016/j.cell.2018.05.048

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.