• About the course

    Course contents

    In this course, you will learn how to analyse single-cell RNA-seq data using the Seurat single cell tools integrated in the easy-to-use Chipster software. The exercises and course data are based on the Seurat guided analyses "Guided tutorial - 2700 PBMCs" and "Stimulated vs Control PBMCs".

    You will learn the following topics, and how to perform these steps in the Chipster software:

    • UMAP plot showing how cells (dots) are clusteredperform quality control and filter out low quality cells
    • normalize gene expression values
    • scale data and remove unwanted sources of variation
    • select hihgly variable genes
    • perform dimensionality reduction (PCA, tSNE, UMAP, CCA)
    • cluster cells
    • find marker genes for a cluster
    • integrate two samples
    • find conserved cluster marker genes for two samples
    • find genes which are differentially expressed between two samples in a cell type specific manner
    • visualize genes with cell type specific responses in two samples

    "It is so nice to be able to do the whole workflow in Chipster, compared to the old model, where I had to transfer the tsv file to R-studio and run Seurat there. -- I learned how to use the Seurat tools in Chipster and what all the steps really mean. I learned to check the results after every step to adjust the next steps parameters and to test different PCA plotting tools. I also learned how to find different genes in the clusters and how to visualize them. I never got this far using the R-pipeline. " -Pinja, course participant & PhD student from University of Helsinki



    Learning objectives

    After this course you should be able to:

    • use the Seurat tools available in Chipster to undertake basic analysis of single cell RNA-seq data
    • name and discuss the different steps of single cell RNA-seq data analysis
    • understand the advantages and limitations of single cell RNA-seq data analysis in general and in Chipster

    Keywords: Chipster, Seurat, single cell sequencing, RNA-seq, clustering, aligning cells, cluster markers


    Links to material
    The relevant material is linked in each course section. Here are some quick links:


    Practicalities
    Each section of this course contains lecture videos, hands-on exercises and questions/tasks. The tasks can be used to confirm that you have reached the learning goals. You can use the Q&A Forum below to ask questions regarding the course topics or the exercises. Once you have finished all the tasks, you can download a course certificate with a unique course identifier. You can follow your progress with the progress bar on the right. The estimated time to complete the course is 2-3 days. In the certificate we recommend granting 1 credit (ECTS) for the course. In practical matters, please contact event-support (at) csc.fi, and in content related questions, chipster (at) csc.fi.
  • Course certificate and feedback

    Congratulations on completing the course! 

    You can download the course certificate from the link below, after you have finished all the sections, including giving course feedback, and the tasks/quizzes.

    We are actively developing both the course contents as well as Chipster software, so please 

    • give us feedback (you can find the link below) 
    • write your thoughts on Chipster in the forum below.

    Need help?

    • If you have any questions or you need support with Chipster, feel free to e-mail us at chipster@csc.fi
    • Practical/technical questions regarding the course can be sent to event-support@csc.fi

    Accessing the course materials after the course?

10. Test your skills