5 Terms You Need to Know in Cytobank
So you’ve signed up for Cytobank and you’re logged in for the first time. Now what? Here are 5 terms to learn when starting to use Cytobank.
Don’t forget: we also have video tutorials providing a general overview of Cytobank and covering these concepts in more detail.
The Inbox is the first page to which you are directed upon signing in to Cytobank.
It contains a list of your uploaded experiments, experiments other users have shared with you, and public experiments. Much like an email inbox, you can tag experiments with labels for filtering and use the search box to further filter results. Clicking on an experiment name will direct you to the Experiment Details page, from where you can access your Illustrations.
An Illustration contains the data plots associated with your experiment. You build Illustrations from an experiment’s Working Illustration page, which is accessed from the Experiment Details page to which you are taken upon opening an experiment from the Inbox. (In other words, go to Inbox -> click to open an experiment -> click on “Working Illustration”.)
It is within the Working Illustration that you will define cell populations, annotate samples, and build your plots. Saved Illustrations can be accessed from the Experiment Details page. You will use Figure Dimensions to construct your Illustrations (see below).
3. Figure Dimensions
Figure Dimensions are the attributes that define and categorize the FCS files in your experiment. You will use Figure Dimensions to organize the display of the plots in the Illustration you construct. For example, you can:
* Tell Cytobank which files are associated with which stimulation conditions using the “Conditions” Figure Dimension
* Assign timepoint labels to FCS files using the “Timepoints” Figure Dimension
* Define populations by drawing gates using the “Populations” Figure Dimension
* Label channels and define staining panels using the “Channels” Figure Dimension
If you have entered descriptive Sample ID or Tube Name information while collecting your samples on the flow cytometer, Cytobank will automatically filter your FCS files into the appropriate category once you have created the label within the Figure Dimension, saving you a lot of time annotating sample files!
Each orange-colored Figure Dimensions box can be clicked and dragged to a new position, which rearranges the display of the plots in the Illustration based on the position of each Figure Dimension box. Don’t forget to update the Illustration to see the results!
4. Channels and Panels
The term “Channels” refers to the flow cytometer channel on which your data were collected. If you used different detection reagents on the same channel for different samples (e.g., pERK1/2-PE for some samples and pAkt-PE for other samples), you can define staining “Panels” to group the samples accordingly.
Annotation refers to the assignment of files to Figure Dimensions (see Concept #3). Annotating your files (i.e., telling Cytobank what they are!) is the first step you will take upon entering the Working Illustration. Annotation can be a one-time event, and once you have completed it, you can easily switch between plot layouts and types (dot plots, heatmaps, histogram overlays) with the click of a button.
You can also find these explanations on our documentation site, listed under Basic Cytobank Concepts. More questions? We’re happy to help. Send us an email or submit a support ticket while logged into Cytobank.