MIAMExpress Submission Guidelines

In this help page:

• Overview
• What you need to submit
• Getting started
• Protocol submissions
• Array design submissions
• Experiment submissions
• Supported data file formats
• Experiment diagrams

Overview

MIAMExpress is a web based tool for submitting microarray data and microarray designs to the ArrayExpress database. It is suitable for submitting both single-channel (e.g. Affymetrix) and 2-channel data.

MIAMExpress can be used for experiments up to 50 hybridizations in size. For larger experiments please use the spreadsheet submission systems. You must also use the spreadsheet submission systems for Illumina, Nimblegen and UHTS data and for cases where you have more than one raw or normalized data file per hybridization.

The MIAMExpress login page is here:
MIAMExpress login page >>

What you need to submit

To submit data using MIAMExpress you'll need to provide the following information:

• protocols describing your sample growth/treatment and processing steps
• array design layout information if it was custom or self spotted (commerical array designs are already in ArrayExpress)
• experiment information
  • details of all the samples used in your experiment
  • 1 raw data file (e.g. CEL, gpr, txt) for each hybridization you performed
  • 1 normalized data file per hyb and/or a combined data file (processed data is optional but required for full MIAME compliance)

This information is submitted in the following order:

Getting started

From the MIAMExpress home page follow the 'submissions' link to get to the login page:
MIAMExpress login page >>

If this is your first MIAMExpress submission click the 'Sign up new submitter' button to create an account for yourself.

Login to MIAMExpress and then select the type of submission you want to make.

Protocol submissions

After logging into MIAMExpress click on 'Protocol submission'. Only create protocols that are relevant to your experiment.

1. Use the 'Create new...' buttons to create the protocols used in your experiment.
2. Change the automatically generated protocol name like 'Treatment protocol 55741' to something meaningful, E.g., 'WilliamsLab high salt'
3. Complete the requested information in the protocol forms then click 'Submit' to save it.

You will be able to select your saved protocols when making your MIAMExpress experiment submission. You only need to submit your protocols once and you can then re-use them in future MIAMExpress experiment submissions. Protocols for Tab2MAGE/MAGE-TAB submissions are created separately.

Protocol types

• Array - describe how your array design was produced if it is custom or self spotted.
• Sample Growth Conditions - describe how your samples were grown or obtained.
• Sample Treatment - describe any treatments applied to your samples as part of the experiment.
• Pooling - if your experiment included pooling of material from multiple samples create a pooling protocol to describe this.
• Extraction - describe how DNA, RNA or protein was extracted from your samples.
• Labeling - describe how your DNA, RNA or protein was labeled. Standard Affy protocol already created.
• Hybridization - describe how your hybridizations were performed. Standard Affy protocol already created.
• Scanning - say which scanner and scanner settings you used. Standard Affy protocol already created.
• Normalization - if you will be providing a normalized data file for each hyb describe your normalization method here. Standard Affy protocol already created for CHP files.
• Transformation - if you will be providing a single file containing processed data from all your hybs describe how this data was calculated here

After submitting your protocols return to the 'Submission types' page and make an array design submission (if required), then start your experiment submission.

Array design submissions

If you have used a self-spotted or custom array design you'll need to submit the array layout and annotation to us so start an array design submission. If you have used a commercial array design (e.g. Affymetrix, Agilent, Illumina) that it is already described in ArrayExpress you can skip this step. There is information on which array designs are in ArrayExpress and how to submit new designs here:
Array design submission help >>

Experiment submissions

After logging into MIAMExpress click on 'Experiment submission'.

The experiment submission is where you describe your experiment, samples and hybridizations and then upload your data files. You will select the relevant protocols that you've already created, and the name of the array design used.

There are two interfaces to the MIAMExpress tool which you can select from the Experiment submission page.

• the batchloader interface where you fill in your experiment information in a spreadsheet-like format.
  • Full instructions on using the MIAMExpress Batch Upload Tool >>

• the web page interface in which a series of web forms are filled out. This can be time consuming for large experiments.
  • Full instructions on using the MIAMExpress web form interface >>

In both the order of information entry is as follows:

Here are some definitions of the terms used in MIAMExpress:

• Experiment - the complete set of hybridizations performed in a study.
• Experimental Factor - a property which varies between samples and is important in the interpretation of your data, e.g. time, compound, genotype.
• Sample - a biological material used in the study, e.g. a mouse, a tumor sample, a bacterial culture, a group of seedlings. You'll need at least one sample for each condition studied. If your experiment includes biological replicates create a sample for each biological replicate. If your experiment uses a common reference such as Universal Reference RNA remember to create this as a sample too.
• Extract - the RNA, DNA or protein extracted from a Sample.
• LabeledExtract - RNA, DNA or protein labeled with a particular dye such as biotin or Cy3.
• Hybridization - a single array or chip which has one or two LabeledExtracts hybridized to it.

After completing your experiment submission:

• You'll receive an immediate confirmation email from MIAMExpress and your submission will be locked so that you cannot edit it. If you need to edit the submission after this time please email us at .
• The curation team will review your submission and will send you an accession number when all required information has been provided. Email us if you have an questions

Supported data file formats

This table shows what data files you can submit using the MIAMExpress submission tool. Do not edit your raw data files. There are definitions and more information on how to format normalized and combined data here:
Data file help page >>

The following cases are NOT SUPPORTED by MIAMExpress:

• 2-channel Nimblegen data (2 raw data file per hybridization)
• Illumina data
• UHTS data
• Missing raw data files for some or all hybs
• More than 1 raw data file per hyb (e.g. multiple scans per hyb, or 2-channel ImaGene data where you have a separate data file for each channel)
• More than 1 normalized data file per hyb
• More than 1 combined data file per experiment

In these cases use our spreadsheet submission systems to submit your experiment and protocols to ArrayExpress.

Experiment diagrams

MIAMExpress includes a visualization tool which will produce a diagram showing the links between your samples and hybridizations.

To view an experiment diagram showing everything you have created so far:

• In the batch upload tool click the 'Visualize submission' button on the toolbar
• In the web forms click the 'Visualization: PNG ' link at the top of any page in an experiment submission

The diagram shows each component in the experiment submission as a box - if you are using the web form interface you can click on these boxes to take you to the form describing that component.

The diagram shows, from left to right:

Experiment -> Samples -> Extracts -> Labeled Extracts -> Hybridizations

The colour of the box around each labeled extract indicates which dye it was labeled with (blue=biotin, red=Cy5, green=Cy3).

Example diagram for 2-channel experiment with dye swap (2 samples, no biological replicates):

Example diagram for 2-channel experiment with common reference (2 experimental samples, 1 reference sample, no replicates):

Any further questions, please see our FAQ.