Section: 10. Annotate cells and clusters | Single-cell RNA-seq data analysis with Chipster | csc

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  • 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 "Introduction to scRNAseq integration".

    This course contains two types of lecture videos: short lectures on each topic by trainers from CSC (ELIXIR-FI), and more in-depth lectures by Paulo Czarnewski (NBIS / ELIXIR-SE), Ahmed Mahfouz (LUMC / ELIXIR-NL) and Jules Gilet (ELIXIR-FR).


    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 (with global scaling normalization and SCTransform)
    • scale data and remove unwanted sources of variation
    • select highly variable genes
    • perform dimensionality reduction (PCA, tSNE, UMAP, CCA)
    • cluster cells
    • find marker genes for a cluster
    • annotate cells and clusters using a reference data
    • take a closer look at the Seurat objects
    • 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.  


    Help
    In practical matters, please contact event-support (at) csc.fi, and in content related questions, chipster (at) csc.fi. You can also join the Weekly CSC research user meetings in Zoom to discuss course matters and get help with the exercises.

10. Annotate cells and clusters

  • 10. Annotate cells and clusters

    In this section, you will learn how to annotate the cells and clusters in your data using SingleR tool and CellDex reference datasets.

    After clustering, we want to know what kind of cells the clusters consist of. One way is to look at the differentially expressed genes between the clusters, and based on those and known cell type biomarkers to label the clusters manually. Another approach is to compare the cells to a reference dataset with cell type labels. In Chipster, we offer SingleR tool and CellDex references for this purpose. 

    First, watch this lecture video about SingleR annotations:

     

     

    You can also check the manual for SingleR.

    Next, do the following exercises in Chipster:

    1. Annotate clusters

    Choose seurat_obj_clustering.Robj generated in the clustering step. Run tool SingleR cluster annotation.

    Open singleR_annotations_plots.pdf and see how the clusters are annotated. What are the cells in cluster 3 (the cluster that is far from the other cells)? When annotated cluster-wise, do some clusters get the same label? Does the cell-wise annotation reveal more about those clusters? Looking at the heatmap, do some labels look more similar to each other? 

    2. Rename clusters

    Select again the seurat_obj_clustering.Robj and rename_clusters.tsv file (given together with the original input tar file, so you can find it most likely at very top of the workflow view, or you can use the "Find file" option) which contains the manually picked cluster annotations based on marker genes from the Seurat vignette. Check that the files are correctly assigned. Run the tool Seurat v4 -Rename clusters and open the result file clusterPlotRenamed.pdf.  How well do these annotations match with what you got from SingleR in the previous exercise (that is, do the automatic SingleR annotations agree with the labels given by the Seurat developers)?

    Finally, answer the questions in the quiz.