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TABLE 1: Example Subset of the Study File Format

A

B

C

Source Name

Material Type

Characteristic[cell type]

LLC-PK1

biospecimen

porcine proximal tubule cells

LLC-PK1

biospecimen

porcine proximal tubule cells

Fields

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 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. If the sample assayed is a nanoparticle sample or some chemical substance not derived from a biological material, then the corresponding source name should refer to the starting sample that was modified by a protocol for the assay. Source names can be qualified using the following column attributes: Characteristics characteristics [ ], Material Typematerial type, Providerproviderand Comment 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: Characteristics  characteristics [ ],  Material Type, Provider, and Comment material type, and comment.

Attributes of Study Nodes

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Material Type---An attribute for the Source Name or Sample Name source name or sample name (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 term accession number and term source REF.

Characteristics [ ]---An attribute for Source Name and Sample Name source name and sample name. The term for each characteristics [ ] attribute is written within brackets (for example, Characteristics [organism], Characteristics [cell type], etc.).

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

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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 (for example, the date when a sample was received from a vendor), one should create a Comment comment [ ] column and specify the type of date within the square brackets (e.g., Comment [date received]).

Parameter Value [<parameter name]---Value of a parameter, which is kept constant, when applying a protocol. The parameter name is written within brackets and must match the term used as value for the Study Protocol Parameter Name study protocol parameter name in the ISA-TAB-Nano investigation file.

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Unit---The standard of measurement used if the values for Characteristic characteristic [ ], Parameter Value parameter value [ ] or Factor Value factor value [ ] columns are quantitative and dimensional. If the term for Unit unit is taken from an ontology/controlled vocabulary, then its Term Accession Number term accession number and the Term Source term source REF should be defined in the ISA-TAB-Nano Study File.

Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value in Source Name, Material Type, Characteristics source name, material type, characteristics [ ], Parameter Value parameter value [ ], Unit unit or Factor Value factor value [ ] columns.

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 term source name field in the ISA-TAB-Nano Investigation file.

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Factor Value [<factor name>]---The value of an experimental independent variable manipulated by the investigator experimentalist with the intention to affect the subject of study (e.g. that is, stressor). Factor names 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 existsComment fields should be attached to the closest node or the closest field.

Files

The Study File Examples, Template, and Glossary are provided below.

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