Frequently Asked Questions (FAQ)

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1. Using ArrayExpress

Searching and understanding data
Data access policy - permissions and restrictions
FTP data download and programmatic access
Other general questions

2. Submitting data to ArrayExpress

Accession numbers
Keeping unpublished data private
Public release date
Which files to submit
Making changes to data already submitted to Arrayexpress

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1. Using ArrayExpress

Searching and understanding data
  • How do I search the ArrayExpress database?
    For simple keyword search, please see the search help page or try our interactive free tutorial. For more complex search queries, e.g. "Find all RNA-seq experiments studying diabetes in mouse", you will need to use some search filters to limit the search space of your keywords, e.g. where "diabetes" is the subject of investigation, and not merely mentioned in background information of a study. Please refer to the advanced search help or this interactive free tutorial.
  • Can you guide me through the table of experiments I get after searching ArrayExpress?
    This online training page will get you started.
  • How do I link sample and data file information in the downloadable files?
    Samples and data are linked together in the samples table on the ArrayExpress website. The table (called the SDRF, which stands for "Sample and Data Relationship Format") can be downloaded as a .txt spreadsheet, which will open nicely in any spreadsheet programme such as Microsoft Excel. To fully understand an experiment, we recommend that you check out also the experiment overview too.
  • I read a paper that referred to data in ArrayExpress but when I searched for the data I got no hits. Why?
    It could be that the submitter of the data has not informed us that the experiment should be made public. Please email us at arrayexpress@ebi.ac.uk with the literature citation where you spotted the ArrayExpress accession, and we will make the data public.
  • I have seen ArrayExpress experiment accessions with prefixes such as "E-MTAB", "E-GEOD", etc. What do the prefixes mean?
    The prefixes indicate the source and/or submission route from which the data came from. The common ones are:
    • MEXP = data submitted via the MIAMExpress submission tool (discontinued since July 2014)
    • TABM = data submitted via the Tab2MAGE submission tool (discontinued since January 2012)
    • MTAB = data submitted via the MAGE-TAB submission tool (discontinued since September 2014) or Annotare
    • GEOD = data imported from NCBI Gene Expression Omnibus
    See the accession codes help page for more information.

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Data access policy - permissions and restrictions
  • Are there any restrictions on the use of data obtained through ArrayExpress?
    No restrictions, all public data from ArrayExpress can be used by anyone and our services are completely free of charge.
  • Do I need a login account to view or access data in ArrayExpress?
    For public data, no login is required. All public data is available to everyone. For private, pre-published data, we provide login accounts to data submitters so that they, and their reviewers, can access them.
  • I've lost my ArrayExpress website login details. What do I do?
    * Note: you do not need an ArrayExpress login for accessing public data. * If you are viewing a curated experiment which you submitted to ArrayExpress, use the forgotten password reminder form in the login box.

    If you are the reviewer, then please contact the journal editor. We can only give ArrayExpress login details to the data depositor directly.

  • I'm reviewing a paper. How do I get a login to view private data that the authors have deposited in ArrayExpress?
    Reviewer login details are sent to submitters on completion of the processing of their submission. Please contact the journal editor to request this login information. We cannot disclose login details to reviewers without first getting authorisation from the submitter or journal.
  • Will I have full access to an experiment while it is private in ArrayExpress?
    Yes, if the experiment is a microarray study. You can view the ArrayExpress record and download all associated files if you log in to ArrayExpress with a data-access account.

    No, if the experiment is a sequencing study. When you log in to ArrayExpress, you will be able to see the full ArrayExpress record, and download processed data files, but the links to raw read data files (in fastq format) are placeholders until the experiment is made public. The reason is that raw data files are brokered to the European Nucleotide Archive (ENA), which is part of the Sequence Read Archive (SRA), a collaboration between ENA (EBI), Genbank (NCBI), and DDBJ (Japan). There is currently no infrastructure to access privately held data files in SRA.

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FTP data download and programmatic access
  • Is there an FTP site to download data files in bulk?
    Yes, all the data and array designs in ArrayExpress are available for direct download. Please see help on FTP downloads.
  • Do you have any application programming interfaces (APIs) for accessing ArrayExpress?
    Yes, we have a REST/JSON API. See Programmatic access for details.

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Other general questions
  • How much overlap is there between ArrayExpress and the NCBI Gene Expression Omnibus (GEO)?
    We import data on a weekly basis from NCBI Gene Expression Omnibus (GEO). All experiments imported from GEO have accession numbers in the format of E-GEOD-n, where n is a number. For example, GEO accession "GSE29080" would become "E-GEOD-29080" in ArrayExpress. As of 6 Apr 2017, ArrayExpress contains 59285 GEO series (experiments), that is about 71% of the 83303 public series available from GEO on the same day. GEO currently does not mirror ArrayExpress experiments systematically. See the GEO data import page for more details.
  • How do I cite my ArrayExpress data sets in my publication?

    You should include your experiment accession number and the URL to ArrayExpress home page, www.ebi.ac.uk/arrayexpress. e.g. "RNA-seq data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress)under accession number E-MTAB-xxxx." You can also include a direct link to your experiment or array design. For example, the link would be https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1234 for experiment "E-MTAB-1234", or https://www.ebi.ac.uk/arrayexpress/arrays/A-MTAB-567 for array design "A-MTAB-567".

    If you wish to include a citation for the ArrayExpress database, then the following publication should be used: Kolesnikov N. et al. 2015 ArrayExpress update - simplifying data submissions. Nucleic Acids Res, doi: 10.1093/nar/gku1057. Pubmed ID 25361974.

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2. Submitting data to ArrayExpress

Accession numbers
  • I urgently need an accession number to include in my publication - how can I get one?
    Firstly, start your submission if you have not already done so! ArrayExpress does not provide accession numbers in advance of submission of data. This is in line with the NCBI Gene Expression Omnibus (GEO)'s policy of provision of accession numbers after deposition.
  • After I've submitted my experiment, how long will it take to get an accession number?

    On average, within 30 minutes. It all depends on the size of your data files, and how busy we are with submissions on a given day. Normally, you should receive an automated email with the accession number within 5 minutes (small microarray experiment) or up to 24 hours (large sequencing experiment). Please email us at annotare@ebi.ac.uk , citing your experiment's title, if the automated email has not come through after a prolonged wait.

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Keeping unpublished data private
  • Can my data be kept private after I submit it?
    Yes, all submitted information will be kept private until the release date that you set at the time of submission, or until a publication is released that contains the ArrayExpress accession number relating to your data. You can also change the release date to suit the peer review progress of your paper. Please see our data availability page for more information.
  • The journal I am submitting to has requested private access to my data - how do I get an ArrayExpress login for them?
    Firstly, start your ArrayExpress submission if you have not already done so! You will be sent login details for viewing your private experimental data on the ArrayExpress website only when curation is finished and when your data is loaded into the ArrayExpress database. If you are really pushed for time and are struggling with your ArrayExpres submission, let us know and we will try our best to help.
  • The journal I am submitting to supports "double-blind" peer review. Can ArrayExpress hide my name and contact details from the reviewers?
    Yes. If you're submitting a new data set via Annotare, simply check the Hide my identity from reviewers box on the Experiment Description page. Please see submitter's guide on anonymity for more information.
    If you are the submitter of a previously non-anonymised private data set in ArrayExpress and would like to switch on anonymity, please write to us at arrayexpress@ebi.ac.uk.
  • I tried to login to ArrayExpress to see some recently submitted private data but it said my username and password were invalid. Why?
    Possibly you have tried to login with your submitter account with our submission tools, such as Annotare? These "submitter" accounts can only be used for submitting data, not viewing it in ArrayExpress. We will provide you with an ArrayExpress data access login account after your submission has been curated and loaded into ArrayExpress.

    If you are using an ArrayExpress login which you have just received, it might not be working yet because ArrayExpress is updated only once a day at about 6am UK time. Try again after this time.

    If you've forgotten or lost your access account details, you can retrieve it using the forgotten password tool. If it still does not work, contact us at arrayexpress@ebi.ac.uk and tell us what login details you are trying to use / which page you tried those details on.

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Public release date
  • I don't know when my paper will be published so what should I put as the release date?
    Enter an estimated public release date up to 1 year in the future from the day of submission. The release date can be changed during/after curation for multiple times to match the peer-review progress. Avoid setting release date at public holidays (e.g. Christmas/New Year period) to avoid inadvertent release of your data. Please see our release date change page for more information.
  • My paper is about to be published - how do I make the data public?
    You can change the release date using this self-service tool. Simply login with the data access account details which we emailed you when curation was completed, double-click at the private experiment that you would like release date changed, and follow on-screen instructions. You would normally have used these account details to log in to the ArrayExpress website and view your private experiment(s). Don't worry if you have forgotten the username and/or password, you can retrieve login details using your submitter's email address and the experiment accession number. Your experiment will appear on the ArrayExpress website at about 6am UK time the following day, after an overnight website update.
  • My paper has been published - how do I add the citation details to my experiment?
    You can add, remove or edit citation details for your experiment using this self-service tool. Simply login with the data access account details which we emailed you when curation was completed, double-click at the experiment that you would like associate the publication with, and follow on-screen instructions. You would normally have used these account details to log in to the ArrayExpress website and view your private experiment(s).

    Don't worry if you have forgotten the username and/or password, you can retrieve login details using your submitter's email address and the experiment accession number. The changes you make will appear on the ArrayExpress website at about 6am UK time the following day, after an overnight website update.

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What data files to submit
  • Which data files do I need to submit for an experiment?
    The files required depend on the technology (e.g. microarray vs sequencing) and also the biological context of the study (e.g. single-cell RNA-seq requires some extra files). Please refer to the submission overview page, which will guide you through the different scenarios.
  • I have MAGE-ML/MAGE-TAB files generated from in-house pipelines. Does ArrayExpress still accept them?

    MAGE-ML files are no longer supported or accepted by ArrayExpress since 2011. MAGE-TAB spreadsheets, provided they are correctly formatted and uploaded via FTP, are still accepted in some exceptional cases under prior agreement with some submitters.

    The easiest way to submit data is to use our latest submission tool Annotare, which will generate MAGE-TAB files for you, so you don't have to worry about learning the file format. All you need to do is to fill in a series of webforms and upload data files within the tool. Annotare also has a built-in validator to save you writing validators/parsers to check your submission.

    If you would like to update your pipeline to generate MAGE-TAB files, please write to us at annotare@ebi.ac.uk to discuss further.

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Making changes to data already submitted to ArrayExpress

  • I hit "Submit" at the end of my submission but I haven't actually finished editing. I logged in to the submission tool but can't edit my experiment anymore. Help!
    Email us at annotare@ebi.ac.uk as soon as possible and ask us to "reopen" the submission and "assign" it back to you, so you can edit it again. (Submitted data sets are "read-only" to the submitter to avoid confusing, concurrent editing of the same submission by submitter and curator.) Remember to include your username and the experiment/array design title in your email so we can quickly find your submission.
  • My data has been loaded into ArrayExpress but I need to change/correct something - how do I do this?
    Email us at annotare@ebi.ac.uk with the accession number and describe what corrections you would like to make. Please see this help page on updating experiments/array designs for further details.
  • My contact details have changed, how do I update them?
    Send your new contact details to us at arrayexpress@ebi.ac.uk and we will change them in ArrayExpress.

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