Skip to content

Publishing Data to Public Repositories

Publishing to public (EBI) repositories should be done as you start drafting your paper. This process may indeed take several days up to a few weeks depending on the complexity of your data, the availability of the MODIS staff and the work load on the EBI side.

Please get in touch with MODIS as soon as you draft your paper. Ideally data should be submitted to public repositories before you submit your manuscript.

MODIS has an extensive experience in publishing NGS data (more than 150 studies published to date) and will perform this as a service, once the data is ready for submission. Importantly, submitting data means submitting datasets with their metadata, which includes links to samples, sample acquisition information, sample processing information (protocols & protocols lists) and general study information.

What is a study?

A study groups datasets of a unique technology (e.g. sequencing) and of unique experimental type (e.g. ChIP-seq). Multi-omics projects involve the submission of multiple studies.

The process to submit data can be sketched out as the following:

  • Preparation meeting with MODIS staff
    • We get to understand your project
    • We explain to you what needs to be done in LabID which usually involves:
      • Grouping datasets into one (or more) studies
      • Annotating samples: MODIS will help you select the relevant and required annotation type and experimental factors.
      • Link Protocols to Samples
  • You perform the modifications in LabID as described in the Data Preparation section
  • MODIS review the study and give you feedback
  • Once everything looks good, MODIS submits the study

Or, if you feel like it, you perform everything yourself as explained in the different sections.

MAGE-TAB format is no longer accepted by EBI's Annotare service

Up to now, MODIS has been publishing sequencing data to ArrayExpress (now part of the EBI's BioStudies) through the Annotare service either using their Annotare user interface (mainly for short single cell studies) or by sharing the data as a MAGE-TAB document (larger studies i.e. more than e.g. 10 samples). As of 1st Apr. 2025, the MAGE-TAB submission route is no longer accepted by EBI's Annotare service. As a result, sequencing data will be submitted to ENA by default. Data submission using the Annotare User Interface remains an option for smaller studies.