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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 141.

TABLE 141: Example Subset of the Study File Format

Fields

ISA-TAB-Nano extends the ISA-TAB specification for the study file by redefining the concept of a sample and adding a new field called MATERIAL FILE to reference the material files that contain description of the material samples.

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 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 biological source from where the sample is derived. 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. Source names can be qualified using the following column attributes: characteristic [ ], material type, material file, provider, and comment. Material Source Name REF---The reference to the material source name specified in the Material file.  The material source name should match the value recorded for Material Source Name in the corresponding ISA-TAB-Nano Material file. The material source name identifies the source from where the material sample is derived.  If the sample assayed is a nanoparticle sample or some chemical substance not derived from a biological material, then the corresponding material source name should refer to the starting sample that was modified by a protocol for the assay.   The material source name column should only be used for physical-chemical or other characterizations in which the material is the primary sample. For in vitro and in vivo characterizations in which the biological specimen is the primary sample, the material should be referenced as a material factor (e.g. Factor Value [material])Source names can be qualified using the following column attributes: characteristic [ ], material type, provider, and comment.

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.

Attributes of Study Nodes

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Characteristic [ ]---An attribute for source name and sample name. The term for each characteristic [ ] attribute is written within brackets (for example, Characteristic [organism], Characteristic [cell type], etc.).Material File---The name of the ISA-TAB-Nano material file that contains detailed descriptions of the source sample. This column is not applicable for biospecimens.

Provider---An attribute for source name, which refers to the name of the person or the vendor providing the source sample.

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Parameter Value [<parameter termname]---Value of a parameter, which is kept constant, when applying a protocol. The parameter term name 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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Factor Value [<factor name>]---The value of an independent variable manipulated by the experimentalist with the intention to affect the subject of study (that is, stressor). Factor terms names are given in brackets, and must be defined in the ISA-TAB-Nano investigation file in the STUDY FACTORS section.

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