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HSLS MolBio Workshops: ChIP-Seq: Partek Flow

Information about hands-on bioinformatics classes

Workshop Objective

This is a 3 hour workshop which provides a brief introduction to techniques, platforms, and methods used in chromatin profiling experiments, including Transcription Factor / Histone ChIP-Seq and ATAC-Seq and also hands-on analysis using HSLS-licensed Partek flow and TRANSFAC/Match software.

Participants will learn how to

  • import NGS reads from an NCBI GEO dataset
  • align ChIP-Seq reads to a reference genome
  • identify narrow and broad peaks from aligned ChIP-Seq data
  • visualize and summarize the output of ChIP-Seq results
  • identify enriched sequence motifs present in peak regions and search for the presence of 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 publication or a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user Interface, so neither computer programming experience nor familiarity with command line interface is required.

PowerPoints

Attribution

Please include the following statement in the acknowledgments section for all publications, posters, and presentations: 

Partek flow software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh was used for data analysis.

The Health Sciences Library System supports the Health Sciences at the University of Pittsburgh.

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