- WHAT: Bulk RNA-Seq
- WHEN: July 15th, 10am-12pm & 1-3:30pm
- WHERE: Online; instructions upon registration
- WHO: Ansuman Chattopahyay & Sri Chaparala
- HOW: Register here
This is a 4½ 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 – 3:30 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
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 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 Summer 2020 MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.
(Photo by Mike Swigunski on Unsplash)