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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Objective

This is a two-part workshop. Part1, the morning session (10 am - 12 pm) 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 (1 pm - 3 pm) focuses on hands-on data analysis practice using HSLS-licensed CLC Genomics Workbench 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 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 Materials

Powerpoints

  • ChIP-Seq data analysis with CLC Genomics Workbench
  • ChIP-Seq data analysis with PartekFlow

Data Download

Software Registration

Databases and Tools

References

Attribution

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

[Software name] licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh was used for data analysis.

If you used the Pitt-CRC server for CLC Genomics Workbench, then please also include the following text in the acknowledgments section for all publications, posters, and presentations: 

This research was supported in part by the University of Pittsburgh Center for Research Computing through the resources provided.

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