Quick Start guide

  1. Browsing and searching
  2. Experiments table
  3. Single experiment overview
  4. Samples table
  5. Downloading files
  6. Submitting data
  7. More help

Under each topic, click on the learn more link to get a bite-size guide from our EBI Train Online tutorial (will open in a new browser window or tab).

 

1. Browsing and searching

You can view all experiments in ArrayExpress by clicking browse on the homepage. You can search for experiments in ArrayExpress by entering keywords or advanced search terms in the search box.

Learn more about searching ArrayExpress.

Browse and search

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2. Experiments table

This is the table of experiments you will see when you search or browse ArrayExpress. Each row represents one experiment. The table will change depending on what you search for and the types of filters used.

Learn more about the experiments page.

Search results table

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3. Single experiment overview

When you click on an accession number in the experiments table, e.g. E-MTAB-3531, you will come to this page which summarises all the information about the experiment and provides links to download the data. There are also links to GenomeSpace and, in some cases, Expression Atlas.

Learn more about the single experiment page.

Single experiment view

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4. Samples table

You'll get to this table from the link "Click for detailed sample information and links to data" on the single experiment overview page, e.g. the samples page for E-MTAB-3085. Here, samples are in rows and sample attributes are in columns. The experimental variable (i.e. the condition being studied) is highlighted in orange. You'll also find direct links to the data files for each sample in the last column.

Use the link at the bottom of the page to download the samples table. This is a tab-delimited text file which can be opened in any spreadsheet program.

Learn more about the samples table.

Experiment samples view

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5. Downloading files

On the single experiment overview page, you can download all files (e.g. sample annotations, raw data files) for the experiment using the links in the "Files" section, e.g. for E-MTAB-3531". For sequencing experiments the raw data files are stored in the the European Nucleotide Archive (ENA) and can be accessed by following the link at the bottom of the single experiment overview page.

Learn more about data files.

Experiment files view

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6. Submitting data

Functional genomics experiments can be submitted to ArrayExpress using our webform-based tool Annotare.

If you are submitting data to us for the first time, you will find guidelines and tips in:

ArrayExpress experiment or array design submission overview

For a comprehensive guide on how to use Annotare see the Annotare help pages. Alternatively you can email us annotare@ebi.ac.uk.

The Annotare submission tool

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7. More help

For a comprehensive guide on using ArrayExpress please try our free, online tutorial:

ArrayExpress: Discover functional genomics data quickly and easily.

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