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Lab 10: RNAseq Analysis

How do scientist and researchers use RNA expression to infer function

Learning Goals

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1. Explain what is meant by the Central Dogma.
2. Define Differential Expression.
3. Explain how mRNA levels in a cell relates to cell function.
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Photo by National Cancer Institute on Unsplash

The Genome is a complete set of DNA instructions to “build” an organism

Image credit:Genome British Columbia

The Central Dogma

• DNA is stored and protected in the nucleus
• DNA is transcribed (copied) to an mRNA molecule
• mRNA is used by the cell to make the proteins through a process called translation

This molecular flow of information is often called the “Central Dogma”.

Image Credit: Concepts of Biology, OpenStax. CC-BY 4.0.

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What do we know about DNA?

• DNA contains all the information to “build” an organism
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• This information can be copied to pass down from generation to generation or during the process of making new cells (e.g. growth).

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• All of your cells have the same DNA information in their nucleus.

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Image Credit.

If all our cells have the same DNA….

Then why do they looks so different and have different functions?

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Figure 16.1 The genetic content of each somatic cell in an organism is the same, but not all genes are expressed in every cell. The control of which genes are expressed dictates whether a cell is, for example, (a) an eye cell or (b) a liver cell. It is the differential gene expression patterns that arise in different cells that give rise to (c) a complete organism.

Image Credit: OpenStax Biology 2e. CC-BY 4.0.

DNA contains recipes for Proteins

• You can think of your DNA (genome) as a Cook Book.

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• This cookbook has about 20,000 recipes to make proteins.

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• What makes each cell different is what combination of the 20,000 recipes are made!

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Differential Gene Expression

• Differential Gene Expression: the process by which cells become different from one another based upon the unique combo of genes that are active or expressed.

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• We can learn about which recipes each tissue type (or even a single cell!) is making by Differential Gene Expression Analysis.

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Studying Gene Expression with RNAseq

• Using sequencing technologies, we can sequence all of the mRNA in a sample. All of the mRNA present in a cell is called the transcriptome.

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• More mRNA for a particular gene = more gene expression (protein being produced)
• Less mRNA for a particular gene = less gene expression (less protein being produced)

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Example workflow for RNAseq

https://en.m.wikiversity.org/wiki/File:RNA-Seq_workflow-5.pdf

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Today we are exploring real data

Alexis Marianes is a student in Allan Spradling lab wants to learn about how the gut functions. Structure tells us about function.

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Take a moment to look at the cells…

What do you notice?

What questions come to your mind?

What can we infer about:

• A gene that expresses in all cells at the same level
• A gene that is very specific in its expression

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Alexis wants to explore...

How are the “recipes” different between these regions?

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More mRNA for a particular gene = more gene expression (protein being produced)

Less mRNA for a particular gene = less gene expression (less protein being produced)

Alexis collects her samples...

Alexis took the flies and cut up the midgut into regions.

Let’s see how this process is done <video>

Now she has 10 samples with different sections.

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Summary

What we learned..

1. Even though all your cells have the same DNA, they are different because of which proteins they make/
2. Generally, information is passed along from DNA to RNA to Protein in a cell. This is called the Central Dogma of Molecular Biology/
3. We can study the amount of mRNA for different genes in a cell to learn which genes are being expressed in a given sample.
4. The different combination of genes expressed in cells are why they “look” different.

What’s next..

1. Excel Spreadsheet Sorting Activity

What we are doing today

Complete the tutorial

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Contributions

This lesson was created by:

• Stephanie R. Coffman, Ph.D. Clovis Community College
• Rosa Alcazar, Ph.D. Clovis Community College

Revised March, 2022

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