European Nucleotide Archive Support

Once sequencing is complete and analysis has been performed, the generated data may be deposited in an archive, such as the ENA (formerly ERA; previously connected to the SRA). The archive requires not only the sequencing data, but the biological metadata associated with the data. To facilitate this process, MISO provides a mechanism to export the appropriate metadata required. This requires adding some extra information to MISO during the sequencing process.

Studies

A study is a unit of work to be submitted to the ENA in a batch. A study in MISO is limited in scope to a project. Although conceptually similar to a subproject, studies exist in MISO solely for ENA support.

Studies List

The studies list can be accessed by clicking the "Studies" link from the ENA list at the left side of the screen. The page shows all of the studies from all projects. At the top of the table, you will find controls for adding, and deleting studies.

You can click on a study name or alias to get to the Edit Study page.

For a particular project, the studies can be found on the Edit Project Page. Click on the "Studies" collapsing section to view the studies table.

Adding Studies

There are two ways to create a study:

  1. Go to the studies list and click the "Add" button in the toolbar at the top of the table.
  2. Go to the project page, expand the "Studies" section and click the "Add" button in the toolbar at the top of the table.

A study can only contain information about samples from a single project. The other information provided in the study description will be included in the metadata sent to the ENA.

Deleting Studies

Studies can be deleted by MISO administrators from either the "Studies List" or the project page. Check the checkbox beside the study and click the "Delete" button from the toolbar.

Experiments

An experiment binds together a study, sequencing platform, and library.

Experiments List

Experiments can be seen in several places:

  • From the "ENA" section on the left, choose "Experiments" to view all experiments. This shows all experiments.
  • From the "ENA" section on the left, choose "Studies", then select the study of interest. This shows experiments associated with this study.
  • From the "Instrument Runs" section on the left, choose "Sequencing Runs", then select the run of interest. This shows experiments associated with this sequencing run.
  • From the "Preparation" section on the left, choose "Libraries", then select the library of interest. This shows experiments associated with this library.

In any of the Experiment lists, you can click on an experiment name or alias to get to the Edit Experiment page.

Creating an Experiment

From the "Instrument Runs" section on the left, choose "Sequencer Runs", and then select the sequencer run of interest. If pools have not already been assigned to partitions, assign them. From the "Experiment" table, choose "Create New". If the "Create New" button does not appear, it is because either there are no pools assigned to the run, or there are no studies for the projects of the libraries connected to this run.

An experiment connects a study to a library on a sequencing platform. Select the appropriate library from the dialog box. A second dialog box will appear with all the studies that belong to the project of this library. Select the appropriate study and provide the title and alias of the experiment. The alias and title map directly to the alias and title in the ENA model.

Once an experiment exists, all sequencer runs of this library from the same platform for a study are connected with this experiment.

Editing an Experiment

Once an experiment is created, the sequencing platform, study, and library it is attached to cannot be changed. However, the name of the experiment and kits used in its production can be edited.

To edit an experiment, find the experiment from any of the "Experiments" lists on the study, sequencer run, or library pages or the complete list of experiments. Click on the name of the experiment. Edit any of the fields and click "Save".

Adding Consumables to an Experiment

The ENA format allows information about the consumables used in the sequencing process. To add kit information, go to the edit experiment page by any of the above methods. In the toolbar above the "Consumables" table, click "Add". In the dialog, select the kit that was used and provide the lot number and date. Click "Save".

This information will be included in the exported metadata.

Deleting Experiments

Experiments can be deleted by their creators or by MISO administrators from the Experiments list page. Select the experiments you wish to delete, then click the "Delete" button in the toolbar at the top of the list. An experiment can only be deleted if it is not included in any submissions.

Once data is ready for submission to the ENA, a submission package can be made. MISO will provide a template for uploading the metadata. These files are not complete. Additional information must be added to describe the files being uploaded.

Submissions

Submissions List

To view submissions, in the "ENA" list at the left side of the screen, click "Submissions".

You can click on a submission ID or alias to get to the Edit Submission page.

Creating a Submission

To create a new submission, in any one of the experiment tables mentioned previously, select the experiments that should be included in the submission and click "Create Submission" from the toolbar at the top of the table.

Enter the title and the alias of the submission and click "Save".

Downloading a Submission

To download a submission package, go to the submission list and click on the submission of interest. From the top right toolbar, click "Download".

Enter the ENA action. If this is the first submission, ADD is the right action. If changing existing data, use MODIFY. Enter the name of your sequencing centre. Click "Download".

This will generate a ZIP file with the XML files needed for submission to the ENA. Extract this archive and add the file information. After modification, the package is ready for submission.

Deleting Submissions

Submissions can be deleted by MISO administrators from the Submissions list page. Select the submissions you wish to delete, then click the "Delete" button in the toolbar at the top of the list.