The Study nodes are denoting the study subjects (biological samples) and the Assay Nodes describe the experiment itself. The samples processing might be more complex than a single step. There could be multiple protocols involved. These could describe biological sample handling, but also data processing. There are means to assign characteristics, protocol parameters and factor.
The named nodes may have additional qualifications * – e.g. Characteristics, Factor values, Material types, Terms (from a defined ontology), Units, etc., as in the next figure. There could be multiple protocols involved (examples follow).
* http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24no... 2.2 Study file. In this file, information is structured on a per-row basis with the first row being used for column headers. The Study file contains contextualizing information for one or more assays, for example; the subjects studied; their source(s); the sampling methodology; their characteristics; and any treatments or manipulations performed to prepare the specimens. See also section 4.2.