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The study file provides a mapping between the samples (biospecimens and material samples) and processing events (occurs whenever a protocol is applied) associated with a study.   It is also used to provide values for the parameters and factors associated with an assay of the sample. In ISA-TAB-Nano, factors can be either entered in the study file or in the assay file.   For physico-chemical characterizations of nanomaterials, the sample is the nanomaterial.   For in-vitro and in-vivo characterizations, the sample is the biological specimen (cell line, animal, and so forth).   The nanomaterial applied to a biospecimen in an in-vitro or in-vivo assay is considered as a study factor along with other factors that vary in the experiment (for example, dose).   The study file is required as it functions as the primary mapping file between the samples and the assay.   For studies involving nanomaterials (also applies to small molecules), the material file allows for a detailed description of the composition and characteristics of the nanomaterial, and the ISA-TAB-Nano material file name is referenced as a qualifier for the source sample (nanomaterial) in the study file.

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The ISA-TAB-Nano study file leverages the ISA-TAB file format, which is a horizontal-based spreadsheet format with column headers in the first row.  An example subset of this format is provided in TABLE  TABLE 14. 

TABLE 14: Example Subset of the Study File Format

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Please note, the concept specified within the bracket “\[ \]” is a  variable depending on the type of sample. According to the ISA-TAB  specification, the Study file has different types of fields called  nodes, attributes of nodes, qualifiers of nodes’ attributes, and other  valid fields.  [TABLES 15 and 16 |ICR:Study File Examples]on the Study Files Examples page provide additional examples of files using these different types of fields.

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_Source Name_\---The unique identification name of the source from where the sample is derived.  Source names can be qualified using the following column attributes: _characteristic_ \[ \], _material type_, _material file_, _provider_, and _comment_.

(1) If the sample assayed is a biological specimen, its source is the starting biological material from which the sample was derived after the application of a protocol. The name of the source typically refers to the cell line or animal number for biological specimens. 

(2) If the sample assayed is a material that is not derived from a biological source, then the corresponding source name should refer to the starting sample that was modified by a protocol for the assay.   In this case, the source name should match the value recorded for material source identifier in the corresponding ISA-TAB-Nano material file.

_Sample Name_\---The unique identification name of the sample. The sample is obtained after the application of a protocol.  Sample names can be qualified using the following column attributes: _characteristic_ \[ \], _material type_, _material file_, and _comment_.

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Material type---An attribute for the source name or sample name (e.g.for example, biospecimen, nanoparticle sample, small molecule etc.).   The term can be a free-text description or taken from an ontology or a controlled vocabulary.   If it is the latter, then the following qualifiers are used:   term accession number and term source REF.

_Characteristic \[ \]_\---An attribute for _source name_ and _sample name_.  The term for each characteristic \[ \] attribute is written within brackets (e.g.for example, Characteristic \[organism\], Characteristic \[cell type\], etc.).

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_Date_\---The calendar day on which the protocol was carried out.  The date format should be in YYYY-MM-DD.  If there are other dates to be recorded (e.g.for example, the date when a sample was received from a vendor), one should create a _comment \[ \]_ column and specify the type of date within the square brackets (e.g., Comment \[date received\]).

_Parameter value \[<parameter term\]_\---Value of a parameter, which is kept constant, when applying a protocol.&nbsp; The parameter term is written within brackets and must match the term used as value for the _study protocol parameter name_ in the ISA-TAB-Nano investigation file.

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Term Source REF---The name which identifies the source from where a term is selected and entered in ISA-TAB-Nano study files.   This name should match one of the names entered in the term source name field in the ISA-TAB-Nano Investigation file.

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_Factor Value \[<factor name>\]_\---The value of an independent variable manipulated by the experimentalist with the intention to affect the subject of study (i.e.that is, stressor). Factor terms are given in brackets, and must be defined in the ISA-TAB-Nano investigation file in the STUDY FACTORS section.

_Comment \[ \]_\---Any comment that provides additional information, which is added only when no other appropriate field exists.

• Study File Examples

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