HSLS MolBio Workshops

This workshop is focused on multiomics data analysis - Spatial Transcriptomics. While CITE Seq enables researchers to capture both RNA and surface protein expression simultaneously, the Spatial Transcriptomics method allows researchers to measure mRNA expression in the spatial context of a tissue.

Participants will learn how to

• import 10x Genomics Spatial Transcriptomics (Visium) data to PartekFlow
• merge expression data with histological information
• filter and normalize the data
• generate UMAP plots to visualize data
• identify cell populations and biomarkers and compute differential gene expressions between two cell populations

Target Audience

Experimental biologists seeking to analyze scRNA-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.

Software Registration

• HSLS Software Registration for PartekFlow and CLC Genomics Workbench

PowerPoints

• Spatial Transcriptomics data analysis using Partek Flow

Data Download (10x Genomics)

• Spatial Transcriptomics - 
  • Normal Human Prostate (FFPE) Spatial Gene Expression Dataset by Space Ranger 1.3.0 
    • Datasets Summary 
    • Feature / barcode matrix HDF5 (filtered)
    • Image file
  • Human Prostate Cancer, Adenocarcinoma with Invasive Carcinoma (FFPE)
    • Datasets Summary 
    • Feature / barcode matrix HDF5 (filtered)
    • Image file

Tutorials/Manuals :

• Partek Flow Manual
• CLC Genomics Workbench Manual 

Webinars 

• Visium Spatial Gene expression method by 10x Genomics
• Spatial Transcriptomic analysis with Partek flow
• Single-cell RNA-seq data analysis with CLC Genomics Workbench

Databases

• Cell Marker - a manually curated resource of cell markers in human and mouse
• Panglao db - a database for single cell RNA seq experiments from mouse and human
• The Human Cell Atlas and The Human Protein Atlas - the expression profiles in single-cell types
• scRNASeqDB -  a database for gene expression profiling in human single cell by RNA-seq
• Single Cell Expression Atlas - single cell gene expression data across species
• Single Cell Portal (Broad Institute) -  portal that contains an analysis of human glioma, immune, and other stromal cells at the single cell level
• Tabula Muris - a compendium of single cell transcriptome data from Mus musculus

Tools

• Cell Ranger and Space Ranger - a set of 10x genomics analysis pipelines that process chromium or visium data
• Azimuth - a tool for rapid mapping of query datasets to references
• Garnett - a tool for automated cell type classification

Recommended Readings:

• Single-cell genome sequencing: current state of the science
• Current best practices in single‐cell RNA‐seq analysis: a tutorial
• Integrated analysis of multimodal single-cell data. Cell 184, 3573-3587.e29 (2021)
• Method of the Year 2020: spatially resolved transcriptomics. Nat. Methods 18, 1 (2021).

Attribution

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

[software name, such as CLC Genomics workbench, Partek Flow ] software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh (RRID:SCR_011975) was used for data analysis.

Feedback

Please evaluate the workshop

scRNA-seq : CITE-Seq and Spatial Transcriptomics data analysis with  PartekFlow

Support

• Request for consultation w/ HSLS-MBIS
• Contact Partek Support Team