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Description

The assay file provides references to assay results including measurements, raw data files, derived data files, image files, and other file types.   There here can be multiple assay files per study.

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The ISA-TAB-Nano assay file leverages the ISA-TAB file format, which is a horizontal-based spreadsheet format with column headers and row values.  An example subset of this format is provided in TABLE 21.  Please note, concepts specified within the bracket “\[ \]” are variables depending on the type of assay.

TABLE 21: Example Subset of the Assay File Format

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ISA-TAB-Nano Extensions---In support of ISA-TAB-Nano, the extensions and constraints in TABLE 2 were applied to the ISA-TAB assay file.   One important extension is that  that ISA-TAB-Nano allows the entry of summary data in the assay files through an optional field called Measurement Value.

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According to the ISA-TAB specification, the assay file has different types of fields called nodes, attributes of nodes, qualifiers of nodes’ attributes, and other valid fields. The assay file supports the following types of information:

•  Source Source or sample name
• Assay protocol reference and protocol parameter values
• Assay name, performer, and date the assay was performed
• Assay factor values including units and statistics, if applicable
• Assay measurement values including units and statistics, if applicable
• Raw data files, derived data files or image files, if applicable

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Source Name---The unique identification name of the source referred to from within the study file.   This column is used only if the source is same as the sample in an assay. Source names can be qualified only using Comment.

Sample Name--- The unique identification name of the sample, which is referred to from within the study file.  The The sample is obtained after the application of a protocol.   Sample names can be qualified only using Comment.

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Material type---An attribute for the sample name (e.g.for example, biospecimen, nanoparticle sample, small molecule etc.) if the same attribute is not given in the study file.   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.

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Date---The calendar day on which the protocol was carried out.   The date format should be in YYYY-MM-DD. 

_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 investigation file.

_Measurement value_ \[<measurement term>\]---The endpoint of the assay. &nbsp;This field is used to capture measurement outputs recorded in summary data.

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_Unit_\---The standard of measurement used if the values for _characteristic_ \[ \], _parameter value \[ \]_ or _factor  value \[ \]_ columns are quantitative and dimensional. If the term for _unit_ is taken from an ontology/controlled vocabulary, then its _term accession number_ and the _term source REF_ should be defined 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.

Statistic---The type of statistical measure attributed to a numerical value (e.g.for example, mean, standard deviation, z-average, etc.). This is a required field, if the parameter value, factor value, or measurement value is a statistical measure.

Other Assay Fields

_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.&nbsp; Factor Value\[\] in assay file should reference technical variations (such as software, instrument or protocol variations).

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

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