Skip to Main Content

HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Objective

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.

Workshop Materials

Software Registration

PowerPoint/Video

Data Download (10x Genomics)

Tutorials and Webinars

Databases and Tools

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 

References

Recommended Readings:

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 & Support