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After reaching an investigation entity (such as investigation, study, assay, source, protocol, sample, or data file), you can download the full data, selected metadata, or selected data associated with that entity. The full data is always associated with the investigation as a whole. 

Also note that if you selected multiple objects to visualize and filter, a download includes all of those objects.

Metadata describes the structure of the data collected in an investigation and translates to the file columns, field definitions, and placeholders that appear in a spreadsheet. It is in Investigation-Study-Assay tab-delimited format (ISA-Tab), which is based on the ISA-Tab specification 

The data files often contain image files and spreadsheets and can be a large file size.

Each download option has a button on the Investigation Details, Study Details, and Assay Details pages.

Image Added

• Download Full Data downloads metadata and data files for the entire investigation. Since this can be a large file size, the file size appears on the button.
• Download Selected Metadata downloads only the metadata of a selection you make after filtering a study an assay.
• Add to Download downloads both the metadata and the data files of one or more selections you make after filtering a study or an assay.