INTRODUCTION TO THE CASE IT SIMULATION

Update 12/9/25: New and revised video tutorials have been added to theCase It YouTube Channel

Begin by watching the video that introduces the Case It interface. Then learn the steps of PCR, restriction enzyme digestion and DNA electrophoresis, as these are basic procedures used in a variety of cases. A quick way to learn these procedures is via the video tutorial PCR: primer visualization, digestion and electrophoresis, also linked in the table below. You can then view Restriction enzyme digestion and DNA electrophoresis Part 1 and Part 2 for more detail. Tutorials for other lab procedures are linked in the table below.

The CRISPR exercise covers steps of restriction enzyme digestion and DNA electrophoresis, using both plasmid DNA and oligonucleotides. This video uses plasmid DNA from that exercise to demonstrate these techniques.

TROUBLESHOOTING: If you run into any issues with the software not working properly (files or folders appear to be empty, error message on startup), move the Case It folder to your desktop, or if it is already on the desktop, create a new folder and move the Case It folder inside it. Avoid nesting the Case It folder inside other folders, and always leave the Case It executable file (Case It v7.0.5.exe) inside the Case It folder.

If you are using the Mac version, read this important information about finding files.

Use the Search box below to see selected results (e.g., try typing ‘video’ or ‘PCR’ in the box).

TUTORIALS FOR CASE ANALYSIS AND RESEARCH APPLICATIONS

Tutorial name	Media	Description
Methods for BLAST, sequence alignment, and tree-building	PDF, Powerpoint	Bioinformatics tutorial covering BLAST and three different methods of sequence alignment and tree-building, using case scenarios as examples.
Searching sequences	PDF, Powerpoint	Tutorial demonstrating sequence searching feature using color vision research project as an example.
Overview of the Case It interface: Data Screen and Lab Bench	Video	IMPORTANT - go through this brief video before using Case It v705.
Overview of the Case It interface: Data Screen and Lab Bench	Video	Restriction enzyme digestion of PCR products, using the Cystic Fibrosis case as an example*.
Restriction enzyme digestion and DNA electrophoresis (Part 1): Nobel Prize-winning CRISPR research	Video	Restriction enzyme digestion and electrophoresis using plasmid DNA sequences and Cas9 enzymes from Part 4 of the CRISPR exercise as an example.
Restriction enzyme digestion and DNA electrophoresis (Part 2): using lambda DNA on both the Lab Bench and Data Screen	Video	Restriction enzyme digestion and gel electrophoresis using virtual tools on the Lab Bench and Data Screen, digesting lambda DNA with three common restriction enzymes. A brief introduction to BLAST analysis is included at the end.
Show forward and reverse primer sites for PCR on any DNA sequence	Video	*Visualization of forward and reverse primer sites for PCR on any DNA sequence. This is part of the video described directly above.
Expression microarray	Video	Background information, loading and running expression microarray cases, connecting to online databases
SNP microarray	Video	Background information, loading and running SNP microarray cases, connecting to online databases, calculations for genotype calling.
Sequence alignment and tree-building via MEGA software	Video	Video tutorial on how to align sequences and build trees quickly, using included MEGA bioinformatics software. Includes information on how to interpret trees.
ELISA Western blot and RT-qPCR	Video	This tutorial has been updated to include modern methods for diagnosing HIV infection, building on a historical example. A surrogate data set is used to demonstrate how viral load is determined.
Dot blot (autoload)	Video	Open and load DNA and probe files quickly and run a Dot blot, using the Breast Cancer case as an example. This is the second half of the Southern and Dot blotting tutorial (starts at 6 minutes in).
Southern blot (autoload)	Video	Select DNA and probe samples and run a Southern blot, using the Huntington’s Disease case as an example. This is the first half of the Southern and Dot blotting tutorial.
Differential display feature	Video	Demonstrates the Differential Display feature used to visually determine the relative amount of DNA in a given band, in Southern blots and gels.
Quantitative PCR (qPCR)	Video, PDF, Powerpoint	How to run qPCR simulation using honey bee case as an example, including calculations for Delta Ct, Delta-Delta Ct, and standard curves.
Notes on program use and terminology	Web page
96-well PCR	Web page	A feature for visualizing qPCR in a 96-well plate to quickly determine viral load for infectious disease cases such as SARS, HIV and influenza. See the qPCR tutorial directly above for a more detailed explanation of the qPCR process, using a honeybee example.
Cytokine ELISA and flow cytometry	Web page	Procedures described in body of mRNA vaccine exercise
Quick start instructions for running microarrays	Web page, Videos	To get up and running quickly with SNP and expression microarrays

How to make screenshots of gels and other images:

Older versions of the Case It simulation had a ‘photo’ feature enabling users to take photos of gels and other images. This feature is no longer supported, so it is necessary to use other screen capture applications, such as those that come with the Windows and Mac operating systems. Snipping Tool (and the newer Snip & Sketch) allows you to capture portions of your screen on Windows computers. Open one of these applications, click ‘New’, and drag the screen to capture an image. The image can then be saved in various formats, although .png is preferred.

For the Mac, one way to capture the screen is to use the Preview application. Open Preview, then select ‘Take Screenshot’ from the File menu. There are three options: From Selection, From Window, and From Entire Screen. The first option is the easiest way to capture an image. The image can then be saved as a .png file. The Screenshot app (formerly Grab) can also be used to capture the screen.