HSLS MolBio Workshops

Gene expression Visualization: Licensed Tools

This 2-hr long workshop focuses on the visualization of gene expression data using HSLS-licensed Partek Flow software.

Participants will learn : 

• Overview of Partek flow
• import RNA-Seq count matrix data into Partek Flow and identify differentially expressed genes
• generate publication-quality graphics such as PCA, volcano plots, heat maps, and Venn diagrams

Target Audience

Experimental biologists seeking to learn how to visualize the 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

• Licensed Tools (PartekFlow) - Presentation Slides

Data Download

• Dex vs. Unt_Matrix - The gene counts for Dexamethasone treatment and Control samples
• DexAlbvsUnt_Matrix (practice) - The practice excercise for students 
• DexAlb Vs.Unt_metadata - Metadata for samples

Software Registration

• HSLS Software Registration - Software registration page on HSLS website

• Overview of Partek flow  - Partek flow tutorials

Selected Tutorials

• Partek flow documentation - Webpage for Partekflow documentation
• Visualizations in Partekflow - Webpage for Partekflow visualizations
• A Web Tool for Generating High Quality Machine-readable Biological Pathways - A publication on JoVE journal 

• BioGRID - A database for Protein interactions
• Reactome - A database for pathways
• Venn Diagram Creator
• BioRender - Scientific illustrations creating tool
• PCA Explained (video)
• Hierarchical Clustering (video) 

• RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells 
• Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 13 (2016). 
• PBMC fixation and processing for Chromium single-cell RNA sequencing 

Feedback

• Class Evaluation

Attribution

Partek Flow

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