ChIP-Seq

Workshop Objective:

This is a 4-hour workshop. The morning session (10am - 12pm) provides a brief introduction to techniques, platforms, and methods used in chromatin profiling experiments, including Transcription Factor / Histone ChIP-Seq and ATAC-Seq. The afternoon session (1pm - 3pm) focuses on hands-on data analysis practice using HSLS-licensed CLC Genomics Workbench, Partek Flow, and TRANSFAC/Match software.

Participants will learn how to

• import NGS reads from a GEO dataset
• align ChIP-Seq reads to a reference genome
• identify and annotate peaks
• visualize and summarize the ChIP-Seq results
• search for known transcription factor binding motifs using TRANSFAC/Match software 

Target Audience:

Experimental biologists seeking to analyze ChIP-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:

• Register for CLC Genomics Workbench
• Register for Partek Flow
• Register for TRANSFAC/Match

Workshop Guide:

• https://hsls.libguides.com/MolBioWorkshops/ChIPseq

Suggested Reading:

• 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.