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Schedule for the single-cell RNA-seq data analysis workshop

Pre-reading

Day 1

Time Topic Instructor
09:30 - 09:45 Workshop introduction Will
9:45 - 10:15 scRNA-seq pre-reading discussion All
10:15 - 10:50 Quality control set-up Noor
10:50 - 11:00 Break
11:00 - 11:40 Quality control: Evaluating metrics Will
11:40 - 12:00 Overview of self-learning materials and homework submission Will

Before the next class:

I. Please study the contents and work through all the code within the following lessons:

  1. Quality control of cellranger counts

    Click here for a preview of this lesson
    We used Cellranger to take our FASTQ files and create counts. There are various metrics presented by this software and it's important to understand how to interpret them as an additional level of QC.

    In this lesson you will:
    - Discuss the outputs of cellranger and how to run it
    - Review web summary HTML report
    - Create plots from metrics_summary.csv file

  2. Theory of PCA

    Click here for a preview of this lesson
    Before we can begin the next steps of the workflow, we need to make sure you have a good understanding of Principal Components Analysis (PCA). This method will be utilized in the scRNA-seq analysis workflow, and this foundation will help you better navigate those steps and interpretation of results.

  3. Normalization and regressing out unwanted variation

    Click here for a preview of this lesson
    During the analysis we will be making lots of comparisons; between cells, between samples, or both. To make accurate comparisons of gene expression we need to first perform normalization. We also want to make sure that the differences we find are a true biolgical effect and not a result of other sources of unwanted variation .

    In this lesson you will:
    - Assess your data for any unwanted variation
    - Normalize the data while also regressing out any identified sources of unwanted variation

II. Submit your work:

  • Each lesson above contains exercises; please go through each of them.
  • Submit your answers to the exercises using this Google form on the day before the next class.

III. Run the code in this script to perform the steps of integration. We will discuss the code and theory in class.

Questions?

  • If you get stuck due to an error while runnning code in the lesson, email us
  • Post any conceptual questions that you would like to have reviewed in class at the end of the homework Google form.

Day 2

Time Topic Instructor
09:30 - 10:30 Introduction to Single Cell RNA-sequencing: a practical guide Dr. Arpita Kulkarni
10:30 - 10:40 Break
10:40 - 11:00 Self-learning lessons discussion All
11:00 - 11:30 A brief introduction to Integration Will
11:30 - 12:00 Running CCA integration and complex integration tasks Noor

Before the next class:

I. Please study the contents and work through all the code within the following lessons:

  1. Clustering

    Click here for a preview of this lesson
    From the UMAP visualization of our data we can see that the cells are positioned into groups. Our next task is to isolate clusters of cells that are most similar to one another based on gene expression.

    In this lesson you will:
    - Learn the theory behind clustering and how it is performed in Seurat
    - Cluster cells and visualize them on the UMAP

  2. Clustering quality control

    Click here for a preview of this lesson
    After separating cells into clusters, it is crtical to evaluate whether they are biologically meaningful or not. At this point we can also decide if we need to re-cluster and/or potentialy go back to a previous QC step.

    In this lesson you will:
    - Check to see that clusters are not influenced by uninteresting sources of variation
    - Check to see whether the major principal components are driving the different clusters
    - Explore the cell type identities by looking at the expression for known markers across the clusters.

II. Submit your work:

  • Each lesson above contains exercises; please go through each of them.
  • Submit your answers to the exercises using this Google form on the day before the next class.

Questions?

  • If you get stuck due to an error while runnning code in the lesson, email us
  • Post any conceptual questions that you would like to have reviewed in class at the end of the homework Google form.

Day 3

Time Topic Instructor
9:30 - 10:00 Self-learning lessons discussion All
10:00 - 11:00 Marker identification Noor
11:00 - 11:10 Break
11:10 - 11:30 Workflow summary Will
11:30 - 11:45 Seurat Cheatsheet Overview and Final Q & A All
11:45- 12:00 Wrap up Will

Answer Keys

Downstream analyses

Differential expression between conditions

Resources

We have covered the analysis steps in quite a bit of detail for scRNA-seq exploration of cellular heterogeneity using the Seurat package. For more information on topics covered, we encourage you to take a look at the following resources:

Seurat-focused

Scaling up: scRNA-seq analysis on HPC

Cell type annotation

Highlighted papers

Other online scRNA-seq courses: