Background
Every study analyzes different variables. Consider the example below, illustrating an experiment with two individuals evaluated against two doses of a drug and two timepoints:
(An example experiment with three variables, individuals, doses and timepoints, and two categories per variable. On the left, the variables and categories are represented. On the right, all possible combinations.)
An experiment such as this would generally be arranged as a grid during sample processing and acquisition (perhaps in a plate or tube rack). The image below illustrates this point and indicates that the experiment would yield eight unique files after acquisition.
(Example plate layout.)
Each file sits at the intersection of three general dimensions or experimental variables: Individual, Dose and Timepoint. Each dimension or experimental variable has attributes or categories associated with it. For example, the Timepoint dimension could have attributes of 15 minutes and 30 minutes. A dimension is generic whereas an attribute is a specific permutation or option of an experimental variable. In the Cytobank platform, these attributes are called sample tags.
Annotating your data with sample tags is how you bring the information about an experiment into a Cytobank analysis, and it is done by a simple process.
How to annotate data with sample tags in the Cytobank platform
Follow the high-level steps below. For in-depth instructions, please check this tutorial article.
1) Understand the number of experimental dimensions. Think about the dimensions as the experimental variables present in the experiment. The example above has 3 (Individuals, Doses, Timepoints). This number will indicate the number of columns you will need to add to the Sample Tag Manager.
2) Add your dimensions. Within the Sample Tag Manager, add the appropriate dimensions for your experiment. For the example in this article, we will use Individuals, Doses and Timepoints. You can also add customized dimensions as shown below.
The set of sample tag types that are available to add in an experiment are:
- the default ones (Conditions, Doses, Individuals, Reagents and Timepoints).
- any custom ones the viewing user has created for that or any other experiment on the server.
3) Create sample tags within dimensions and tag files. Type the necessary attributes or sample tags in the table or copy and paste from an existing spreadsheet. You can also copy and paste from the Sample Tag Manager table or Bulk add tags.
4) Apply changes. Once you have added all sample tags, don’t forget to Apply changes to use the sample tags across the Cytobank experiment.
5) Leverage the sample tags across your analysis in the Cytobank platform. Sample tags will not only help you keep track of your samples as shown below.
(Depending on location within the experimental layout, files are affected by different attributes of experimental variables and thus have different sample tags applied.)
Use sample tags to create meaningful illustrations and to run statistical inference tests.
(Leverage sample tags to create meaningful plots and run statistical analyses. On the left, a comparison box plot representing the median signal intensity of a channel in a population of interest represented without or with sample tags applied. On the right, an example of combining multiple sample tags to represent data analysis results.)
For Research Use Only. Not for use in diagnostic procedures.