- WHAT: Bulk RNA-Seq
- WHEN: Oct 7th, 10am-12pm & 1-4pm
- WHERE: Online; instructions upon registration
- WHO: Ansuman Chattopahyay & Sri Chaparala
- HOW: Register here
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.
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:
Workshop Guide:
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.
HSLS Fall 2020 MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.
(Photo by Mike Swigunski on Unsplash)