3.3 Lab Activity: Biological Databases
3.3.1 Purpose
In this activity, students will learn to search the same online databases used by scientists to collect information about a set of genes and present them to your group. This will give you an opportunity to engage in inquiry-based learning and apply the concepts in molecular biology and genetics from this course.
3.3.3 Activity 1 - Databases
Estimated time: 15 min
3.3.3.1 Instructions
Access the C-MOOR Tutorials
- If you are using SciServer, log into SciServer, click on compute and open your “C-MOOR LearnR” container. Visit SciServer Guides and FAQs if you need to jog your memory on how to do this.
- If you are using AnVIL, log into AnVIL, navigate to your class Workspace, start up an RStudio Cloud Environment, and open RStudio. Visit the AnVIL Guides and FAQs if you need to jog your memory on how to do this. This module can be found in the “3-intro-db” folder of the “rnaseq” curriculum folder.
- If you are using an alternative setup, follow the instructions provided by your instructor.
Start the “Introduction to Biological Databases” tutorial
To move through the activities click “Continue” at the bottom of the screen. When you are done with a topic, click “Next Topic” to move on.
As you complete the tutorial, fill in the table below. This will help you know which database to go back to later on.
3.3.4 Activity 2 - FlyBase
Estimated time: 15 min
3.3.4.1 Instructions
- Start the “Biological Databases: FlyBase” tutorial. On AnVIL, this module can be found in the “4-db-flybase” folder of the “rnaseq” curriculum folder.
- To move through the activities click “Continue” at the bottom of the screen. When you are done with a topic, click “Next Topic” to move on.
3.3.5 Activity 3 - Human Protein Atlas
Estimated time: 15 min
3.3.5.1 Instructions
- Start the “Biological Databases: Human Protein Atlas” tutorial. On AnVIL, this module can be found in the “5-db-hpa” folder of the “rnaseq” curriculum folder.
- To move through the activities click “Continue” at the bottom of the screen. When you are done with a topic, click “Next Topic” to move on.
3.3.6 Activity 4 - Research a Gene!
Estimated time: 45 min
3.3.6.1 Instructions
- Before getting started on this activity, your instructor will assign your group a letter that corresponds to a group of 4 genes.
| Group Assigned Letter |
|---|
- Look up your letter here and write the names of the four genes your group is assigned at the top of each column in the table below.
- In your group, assign each student one of the four genes to research.
| Individual Assigned Gene |
|---|
- Use FlyBase to look up the information in Table 2 below.
- Use HPA to look up the information in Table 3 below.
Table 2. FlyBase Information
| Category | Information |
|---|---|
| General Information | |
| Full Gene Name | |
| FlyBase ID | |
| Sequence Location | |
| Function | |
| Biological Process | |
| Cellular Component | |
| Expression Data | |
| Anatomical Expression | |
| Developmental Stage | |
| Orthologs | |
| Orthologs in other species | |
| Human Orthologs |
Table 3. Human Protein Atlas
| Category | Information |
|---|---|
| Function | |
| Is the gene tissue specific? Which tissue? | |
| Where is it localized in cells? |
3.3.8 Activity 6 - Class Presentation
Estimated time: 30 min
3.3.8.1 Instructions
- With your group, create a short presentation to present your chosen gene to the class.
- Your presentation should have about four slides and be thorough:
- Slide 1: The GENE you picked to share with your group, your name and date
- Slide 2 - 4: Present the information you collected about the gene. For full credit, include relevant images/ diagrams on your slides.
- One student in the group should post your slides on your learning management system (ex. Canvas, Blackboard, Google Classroom) as directed by your instructor to share your findings. Make sure you mention everyone in your group by name so they also get credit for the presentation.