HSLS MolBio Workshops

This workshop is focused on Single cell multiomics data analysis - CITE-Seq and Single Cell ATAC+Gene expression. While CITE Seq enables researchers to capture both RNA and protein expression simultaneously, the Sc ATAC+Gene expresion method allows researchers to measure both chromatin accessibility and mRNA expression at the same time.

Participants will learn how to

• import 10x Genomics CITE-Seq/Sc ATAC+Gene expression data into PartekFlow
• check the quality of the data
• filter and normalize the data
• generate UMAP plots to visualize data
• identify cell populations and biomarkers using multiome data and visualize 

Target Audience

Experimental biologists seeking to analyze single cell sequencing 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

• CITE-seq and Sc ATAC+Gene expression data analysis using Partek Flow PowerPoint
• Single cell Multiomics video - ScRNASeq + Protein 
• Single cell Multiomics video - ScRNASeq + ATACSeq (Partek flow Video)

Data Download (10x Genomics)

• CITE-Seq - 
  • Datasets Summary 
  • Feature/Cell matrix (HDF5) - 5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor with a Panel of TotalSeq™-B Antibodies (v3 chemistry)
• Sc ATAC+Gene expression - 
  • Datasets Summary
    • Datasets - Flash-Frozen Human Healthy Brain Tissue (3k). Single Cell Multiome ATAC + Gene expression

Tutorials/Manuals/Webinars:

• Partek Flow Manual
• Partek flow documentation and videos
   

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
• Tabula Sapiens - a compendium of single cell transcriptome data from Homo sapiens
• Cellstar - The comprehensive database of single-cell transcriptomics annotation resources from multiple organisms

Tools

• Cell Ranger  - a set of 10x genomics analysis pipelines that process chromium data
• Azimuth - a tool for rapid mapping of query datasets to references
• Garnett - a tool for automated cell type classification
• ACT -  Annotation of cell types (ACT): a convenient web server for cell type annotation
• SingleR - Using SingleR to annotate single-cell RNA-seq data
• GPTCelltype - GPT-4 for cell type annotation in single-cell RNA-seq analysis 

Recommended Readings:

• Single-cell genome sequencing: current state of the science

• Single-cell sequencing to multi-omics: technologies and applications

• Integrated analysis of multimodal single-cell data. Cell 184, 3573-3587.e29 (2021)

• Single-cell multiomics: technologies and data analysis methods Nature Review (2020)

• Baysoy, Alev et al. “The technological landscape and applications of single-cell multi-omics.” Nature reviews. Molecular cell biology, 1–19. 6 Jun. 2023, doi:10.1038/s41580-023-00615-w

• singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality

Attribution

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

[software name, such as 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 via the following link:

Single Cell: Multiomics Analysis with PartekFlow Class Evaluation

Support

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