6.1 Background: Single-cell RNA sequencing
6.1.1 Purpose
The purpose of this lab is to introduce single-cell RNA sequencing, how it works, and how it is different from bulk RNA sequencing.
6.1.2 Learning Objectives
- Compare and contrast single-cell and bulk RNA-seq
- Explain what a UMAP plot is and why it is useful for single-cell RNA-seq
6.1.3 Introduction
While bulk RNA sequencing allows us to examine gene expression in a tissue as a whole, newer technologies enable us to look at gene expression in individual cells, opening up new avenues for scientific research. This tutorial will explain the basics of single-cell RNA sequencing and discuss how it compares to bulk RNA-seq. It will also introduce you to UMAP plots - a common method for exploring single-cell sequencing data.
6.1.4 Activity 1 - Biotechnology: scRNA-seq
Estimated time: 15 min
6.1.4.2 Questions
Which of the following steps are typically involved in bulk vs. single-cell RNA-sequencing?
- A) Obtain/dissect sample
- B) Separate cells
- C) Select for mRNA
- D) Convert to cDNA
List the steps involved in each technique.
| Bulk RNA-seq | |
| Single-cell RNA-seq |
Which of the following scientific questions can be investigated using bulk vs. single-cell RNA-sequencing?
- Compare gene expression between healthy and diseased samples
- Investigate gene expression changes as an embryo develops
- Compare gene expression between different cells within a tissue
For each scientific question, state whether it can be investigated with bulk, single-cell, or both, and briefly explain your answer.
| Healthy vs. diseased | |
| Embryo development | |
| Compare cells |
6.1.5 Activity 2 - Introduction to UMAP plots
Estimated time: 10 min
6.1.5.1 Instructions
6.1.5.2 Questions
| Explain why UMAP plots are useful for looking at single-cell RNA-seq data |
|---|
6.1.6 Footnotes
6.1.6.1 Resources
6.1.6.2 Contributions and Affiliations
- Katherine Cox, Ph.D., Johns Hopkins University
- Javier Carpinteyro-Ponce Ph.D., Carnegie Institution for Science
- Matthew McCoy, Ph.D., Stanford University
- Frederick Tan, Ph.D., Carnegie Institution for Science
Last Revised: October 2023