- WHAT: Bulk RNA-Seq
- WHEN: October 2nd, 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
- mport 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 Fall 2019 MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.