Every experiment has variables. Consider the example below, which is illustrating an experiment with two patients evaluated against two doses of a drug at two timepoints:
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.
Each file sits at the intersection of three general dimensions of experiment variables: Patient, Dose, and Timepoint. Each dimension of experiment variable has attributes associated with it. For example, the "timepoints" dimension could have attributes of "15 minutes" and "30 minutes". A dimension is generic whereas an attribute is a specific permutation of an experimental variable. In Cytobank, these attributes are called Sample Tags.
Annotating your data with Sample Tags is how you bring the information about an experiment into a Cytobank experiment, and it is done by a simple process:
How to annotate data with Sample Tags in Cytobank
Follow the high-level steps below. For in-depth instructions, a tutorial article will follow at the bottom explaining exactly how to apply Sample Tags in different ways.
1) Understand the number of experimental dimensions. Think about the dimensions of experimental variables present in the experiment. The example above has 3 (patient, dose, timepoint). This number will indicate the number of Sample Tags dimensions you will need to use.
2) Add your dimensions. Within an Experiment, add Sample Tags dimensions that are appropriate for your experiment. For the example in this article, we will use "Doses", "Timepoints", and "Individuals." You can also add a customized dimension as shown below.
- the default ones (Conditions, Doses)
- any custom ones the viewing user has created for any experiment on the site
- any custom ones that any user has created for that experiment
3) Create Sample Tags within dimensions and tag files. Click into a dimension. Once inside, create the necessary attributes (Sample Tags) and assign the relevant files to them. This is "tagging" the files. For example, this is what the Timepoints dimension would look like in the example experiment above:
4) Repeat. Repeat this process for all necessary dimensions, and you're done! Below is an illustration of the process of annotating by Sample Tags, and how the location of a file at an intersection of experimental variables determines the Tags it gets.
(Depending on location within the experimental layout, files are affected by different attributes of experimental variables and thus have different sample tags applied)