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1.1.1.1       Description

The Study file provides a mapping between the samples, materials, and processing events associated with a study.  Samples can be biological materials (e.g. cell line, animal), nanomaterials, or small molecules.  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, etc.).  The nanomaterial applied to the sample is considered a Study Factor along with other factors that vary in the experiment (e.g. dose).  The Study file is required as it functions as the primary mapping between the samples and the study.  For studies involving nanomaterials, the Material file is references as a qualifier and allows for a detailed description of the composition and characteristics of the nanomaterial.

1.1.1.2       File Format

The ISA-TAB file format leverages a horizontal based spreadsheet format with column headers and row values.  An example subset of this format is provided below.  Please note, concepts specified within the bracket “[]” are variable depending on the type of sample.

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="167332ef-a83a-4df0-a68b-0c35a473dbd3"><ac:plain-text-body><![CDATA[

Source Name

Sample Name

Material Type

Characteristics [organism]

Characteristics [cell type]

]]></ac:plain-text-body></ac:structured-macro>

PK1cell

PK1cell-low-0h

biospecimen

Suis Scrofa

LLC-PK1

PK1cell

PK1cell-low-0h

biospecimen

Suis Scrofa

LLC-PK1

1.1.1.3       nano-TAB Extensions

In nanotechnology, both the material and specimen can function as the primary subject of the study and as such, nano-TAB re-defined the concept of a sample to include both biological specimens and materials.  To accommodate additional metadata needed to effectively describe the material sample, a Material file was introduced.

To accommodate the nano-TAB changes, references to the sample were renamed and are identified as follows:

Field

Change

Description

Field Status

Source Name

Re-defined concept

ISA-TAB definition: starting biological material used in a study.

Nano-TAB definition: The starting material used in a study that is the primary subject of the study.

Required

Sample Name

Support material samples

The sample name typically referenced biological materials.  The sample name can also reference the material identifier

Required

Material File Reference

Addition

Represents the name of the Material file which provides detailed information on the nanomaterial or small molecule

Required for nanotechnology studies

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="3d9b2a8c-bf4b-4679-8a00-1728d34df2e9"><ac:plain-text-body><![CDATA[

Factor Value[nanomaterial]

Addition of [nanomaterial]

References the material identifier of the nanomaterial that is applied to the biological specimen for in vitro and in vivo characterizations.  The

Required for nanotechnology in vitro and in vivo characterizations

]]></ac:plain-text-body></ac:structured-macro>

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