HSLS MolBio Workshops

This workshop briefly introduces methods used in chromatin profiling experiments, including Transcription Factor / Histone ChIP-Seq and ATAC-Seq and also various data integration methods with gene expression data followed by a software demonstration using the HSLS-licensed Partek flow software.

Upon completing this class, you should be able to:

• import ChIPSeq/ATACSeq reads from an NCBI GEO dataset
• align the reads to a reference genome
• identify, annotate and visualize the peaks from aligned ChIP-Seq /ATAC Seq data
• identify enriched known/novel sequence motifs
• integrate with gene expression data
• find enriched gene sets and visualize the results

Target Audience

Experimental biologists seeking to analyze epigenomic data (ChIP-Seq/ATACseq) and also integrate with gene expression 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.

Software Registration

• HSLS Software Registration for PartekFlow 

Powerpoint/Video

• Integrating ChIP-Seq/ATAC-Seq and Gene Expression Data with Partek flow (Powerpoint)
• Integrating ChIP-Seq/ATAC-Seq and Gene Expression Data with Partek flow (HSLS Video)
• Bulk RNASeq and ATAC Seq data integration video   (Partek flow Video)

Data Download

• Dataset : GSE101791 - CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia
  • RNA -Seq - GSE101788 
  • ChIP-Seq (TF/Histone) - GSE101789 
  • ATAC-seq - GSE101790 

Tutorials and Webinars : 

• Partek Flow Manual
• Bulk RNASeq data analysis using Partek flow (Partek flow Training video)
• Partek flow documentation and videos

Databases/Tools :

• Encode : The Encyclopedia of DNA Elements (ENCODE) Consortium is an ongoing international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)
• Cistrome db: an integrative platform for transcriptional regulation studies
• Ensembl Reference Seq Download: download organism's reference genome via a browser from this FTP site
• European Nucleotide Archive; provides a comprehensive record of the world’s nucleotide sequencing information
• Gene Regulatory Elements (GeneHancer) - GeneCards: a novel database of human enhancers and their inferred target genes, in the framework of GeneCards.
• Gene Regulatory Elements (GeneHancer) - UCSC Browser: a novel database of human enhancers and their inferred target genes, available via a genome browser.
• Transfac/Match (GeneXplain): a transcription factor database
• Venn Diagram Creator: a web-based tool to draw custom Venn diagrams.
• SR Tools : SRplot a freely accessible easy-to-use web server that integrated all of the commonly used data visualization and graphing functions

Key References

• Pulikkan JA, Hegde M, Ahmad HM, et al. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018;174(1):172-186.e21. doi:10.1016/j.cell.2018.05.048 (dataset used for the workshop)
• Applications of multi‐omics analysis in human diseases
• Making Sense of the Epigenome Using Data Integration Approaches
• Integrative Analysis of Epigenome and Transcriptome Data Reveals Aberrantly Methylated Promoters and Enhancers in Hepatocellular Carcinoma
• Integration of gene expression and DNA methylation data across different experiments 

• Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation

• Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks

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 (RRID:SCR_011975) 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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