HSLS MolBio Workshops

This workshop will cover processing single-cell RNA-seq data using the HSLS-licensed PartekFlow software. Participants will learn how to  

• import FASTQ/Count matrix files from scRNA-Seq experiments to PartekFlow software
• perform quality checks (QC) on single-cell data 
• filter and normalize the data 
• generate PCA and t-SNE plots to visualize data 
• identify cell populations, and biomarkers 
• compute differential gene expressions between two cell populations and/or multiple samples 

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.

Partek flow

PowerPoints

• scRNA-seq data analysis using Partek Flow 

Lecture Video

• Introduction to scRNA-seq Technologies and Applications (20 min)

• scRNA-seq data analysis from FASTQ reads to count data matrix (Cell Ranger) using PartekFlow (15 min)

• scRNA_seq data analysis starting from count data matrix (43 min)

Data Download

• scRNA-Seq -
  • Human PBMC ScRNA-seq data (1K Cells) at 10X Genomics site - FASTQ and Count Matrix
  • GSE125416  (HDF5; MEX); Single-Cell RNA-Sequencing of Human Embryonic Stem Cell Differentiation Delineates Adverse Effects of Nicotine on Embryonic Development

Software Registration

• HSLS Software Registration for PartekFlow/CLC Genomics Workbench

Partek Flow Manual

Partek flow Webinars

Other useful Vidoes

ScRNASeq Analysis using CLC Genomics Software :

Powerpoint :  scRNA-seq data analysis using CLC Genomics Workbench (03/29/2022)

Lecture video : Introduction to scRNA-seq data analysis using CLC Genomics Workbench (offered on 11/17/2021) (3 hrs)

Additional Datasets :

GSE161267 (MEX); A single-cell atlas of human teeth

CLC Genomics Webinar

• Single-cell RNA-seq data analysis and interpretation

• *Introduction to Single‐Cell RNA Sequencing

• A hitchhiker’s guide to single-cell transcriptomics and data analysis pipelines. Genomics 

• *Current best practices in single‐cell RNA‐seq analysis: a tutorial
• *A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
• Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
• Single-cell RNA sequencing technologies and bioinformatics pipelines
• *CellMarker: a manually curated resource of cell markers in human and mouse
• *PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data
• Integrative single-cell analysis
• Massively parallel digital transcriptional profiling of single cells
• Single-cell RNA sequencing: Technical advancements and biological applications
• Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017).
• Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573-3587.e29 (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 data analysis using PartekFlow

Support

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