- WHAT: Bulk RNA-Seq
- WHEN: February 19th, 10am-12pm & 1-3pm
- WHERE: Scaife Hall, Falk Library, Classroom 2
- WHO: Ansuman Chattopahyay & Sri Chaparala
- HOW: Register here
Workshop Objective:
This is a 4-hour workshop on the techniques, platforms, and methods used in analyzing bulk RNA-Seq data. The morning session (10am – 12pm) 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 bulk RNA-Seq data analysis. The afternoon session (1pm – 3pm) focuses on hands-on practice using HSLS-licensed CLC Genomics Workbench software.
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 quality of RNA-seq data
- align reads to a reference genome
- estimate known gene and transcript expression
- perform differential expression analysis
- discover novel isoforms
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 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 Winter/Spring MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.