• 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:

    • tSNE 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

    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.
  • "Examples are always easier" 

    Now it's time to test what you have learned and analyse your own data! Try analysing some of your own data in Chipster, find some interesting data online, or try starting from the digital expression matrix that is the end result (the 

    digital_expression.tsv file) in example session course_single_cell_RNAseq_DropSeq_done. Don't be scared to face some new issues and try different things -this is an effective way to learn!

    "Beginning is always the most difficult step" 

    Anyone who has analysed some data will tell you the same: cleaning and tuning your data in the very beginning is the most time consuming step. So don't get frustrated! We try to make it as easy as possible, but it's good to practise this as well, as this is often a step that is skipped in course sessions.
    • Read carefully the manual page for the Setup tool 
    • Don't be shy to ask! You can send a support request in Chipster (recommended) or send e-mail to chipster (at) csc.fi
    Your final course task

    After toying around with your data, we would like to see what you came up with! In very free format, please share some of your reports, a print screen of your sessions workflow (keeping in mind that others can see what you are sharing, so no sensitive data obviously), and discuss the following questions:

    • What was different compared to the exercises?
    • What kind of decisions you had to make? 
    • Was there something you were not able to do? 
    • Any error messages you managed to tackle?

9. Comparing two samplesCourse certificate and feedback