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1. Open a Study Details page.
   

   

2. In the Visualize and Select area, click one of the entities.

   Info
   title Study Hierarchy
   The hierarchy of entities for studies according to the ISA-TAB standard is as follows, from less granular to more granular: Source > Protocol > Sample

   For example, click the sourceSource. Metadata for that source appears.

   Info
   Follow this same procedure if you want to filter on Protocol or Sample instead of Source.

   
   

3. From the Source Name list, click the arrow to open the list of values. Each value is a Source Name from the study file, which in this case is s_mrna.txt.
   
4. Click one or more values in the list to select them. To select multiple values, click one, wait for it to appear on the Metadata for Source page, and then click the arrow again to select another value. To clear a selection, click that value again.
   
5. Click Filter Results.
   The Source Count reduces from the 40 original values in the unfiltered study file, s_mrna.txt, to the 3 selected in this procedure.
   
6. Options you have at this point include continuing to explore this data set, downloading the metadata of the 3 values you selected, downloading the selected data of the 3 values you selected (which includes the metadata), or clicking Clear Filters to filter a different entity.

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1. Open an Assay Details page.
   

   

2. In the Visualize and Select area, click one of the entities. Note that the width of some visualizations require you to scroll by clicking the arrows at the bottom of the page.

   Info
   title Assay Hierarchy
   The hierarchy of entities for assays according to the ISA-TAB standard is as follows, from less granular to more granular: Sample > Protocol > Data File

   For example, click the sample. Metadata for the sample appears.

   Info
   Follow this same procedure if you want to filter on protocol instead of sample.

   
   
   
   

3. From the Sample Name list, click the arrow to open the list of values. Each value is a Sample Name from the assay file, which in this case is a_mrna_transcription_profiling_nucleotide_sequencing.txt.
   
4. Click one or more values in the list to select them. To select multiple values, click one, wait for it to appear on the Metadata for Sample page, and then click the arrow again to select another value. To clear a selection, click that value again.
   
5. Click Filter Results.
   The Sample Count reduces from the 39 original values in the unfiltered assay file, a_mrna_transcription_profiling_nucleotide_sequencing.txt, to the 5 selected in this procedure.
   
6. Options you have at this point include continuing to explore this data set, downloading the metadata of the 3 values you selected, downloading the selected data of the 3 values you selected (which includes the metadata), or clicking Clear Filters to filter a different entity.

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1. From the CSSI Data Portal home page, click the Search button.
   
   
   The Search Investigations page appears.
   
   
   
2. In the search box, enter a keyword or phrase. Keywords are any word that appears in the fields belonging to any investigation, study, or assay in the CSSI DCC Portal. This includes all file columns, field definitions, and placeholders that describe the structure of the data collected in this study.
   
   Search results appear immediately, using the context currently in the Search for box, which by default is Investigations. The time the CSSI DCC Portal took to first search for the keyword or phrase and then render the results on the page also appear.
   
   
3. In the Search for box, change the context for your search if desired. Select Investigations, Studies, or Assays. Examples of each search result follow.
   
   In the following example, the keyword is "genomic" and the context is Investigations. Three investigations appear in the search results, along with information about each one that includes the investigation name, number of studies, number of assays, number of files, and description.
   
   
   In the following example, the keyword is "genomic" and the context is Studies. Three studies appear in the search results, along with information about each one that includes the study name, name of the investigation the study is associated with, number of assays, number of files, and description. In these cases, the investigation name and study names are identical.
   
   
   
   In the following example, the keyword is "genomic" and the context is Assays. Three assays appear in the search results, along with information about each one that includes the assay filename, name of the study that the assay is associated with, name of the investigation the assay is associated with, number of files (such as image files), and description.
   
4. Click any investigation name, study name, or assay filename to explore the data further.

Downloading Investigation Data (not yet complete)

You can download selected files, the entire data archive, or only the metadata associated with an investigation. All of the data currently in the portal is public.

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1. Filter the investigation data until you reach the entity you want to download.
   The entity's details page appears. It may involve a selected investigation, study, or assay:
   
   
   Or a process:
   
2. Decide if you want to download the full data, selected metadata, or selected data.
   

To download a single file

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• Your browser's file download dialog box appears, which prompts you to open or save the file.
  

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1. Click the box in the Select File column for any of the files in the list.
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2. Click.
   The Download window appears.
   
3. Enter your email address and click OK.
   The Success window appears.
   
4. Click OK.
5. Look for an email in your inbox with the subject line File Download.
6. Save or open the file.

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