Table 1.

Example of Stratifying, Outcome, and Technical Variables in an Experiment

Stratifying or outcome variable	# in each category
Baseline (pre) or post-therapy	Pre: 40 files Post: 40 files
Therapy response	Responders (R): 28 individuals (2 files each) Non-responders (NR): 12 individuals (2 files each)
Patient ID	40 unique patient IDs (2 files each)
Staining batch (1–4), labeled by date	1 = 20 files 2 = 20 files 3 = 20 files 4 = 20 files

In this example study, patient peripheral blood mononuclear cells (PBMCs) have been acquired in batches for samples pre- and post-therapy. The study outcome variable to be used for CITRUS (highlighted in italics) is therapy response. Timepoint (pre- or post- therapy) is a stratifying variable in this study; one CITRUS run will be performed on the pre-therapy samples, and a separate CITRUS run will be performed on the post-therapy samples. Staining batch will be used to look for batch effects. Timepoint, therapy response, patient ID, and staining batch are annotated by Cytobank sample tags. The number of files expected in each category is outlined in the second column and used to check the files present in Cytobank before starting the analysis