MIAMExpress web interface

In this help page:

• Overview
• Getting started
• Experiment design
• Sample descriptions
• Create Extracts
• Extracts
• Labeled Extracts
• Hybridizations
• Complete submission
• What happens next?

Overview

This web page describes how to submit an experiment to ArrayExpress using the old MIAMExpress web form interface. A MIAMExpress batch upload tool is now available for submitting experiments and we strongly recommend that you use this instead of the web form interface. There are instructions for using the batch upload tool here:
MIAMExpress batch upload tool help >>

If the array design you used is not already in ArrayExpress you must submit it through MIAMExpress before completing your experiment submission:
Array design submission information >>

There is general information about ArrayExpress submissions, accession number assignment and data privacy here:
ArrayExpress submissions help page >>

Getting started

You will need a MIAMExpress login account. If you do not already have one then register here:
MIAMExpress new user registration >>

Login to MIAMExpress:
MIAMExpress login page >>

Click on 'Experiment submission'.
Click the 'Create' button to start a new experiment submission.
To continue with an existing submission, select it from the list and click 'View/Edit'.

Experiment design

Use this form to provide information about your experiment design, add details of any related publication, and create the samples that you used. Provide a meaningful experiment name which includes the information: lab - species - experiment name e.g. Sanger - S. pombe - cell cycle mutants.

• Experiment design type: Select the entries that best describe your experiment. Select one or more terms from the categories biological design, methodological design and technology.
• Experimental factors: Select one or more terms to specify what your experimental factors are. You will be asked to provide values for these factors for each of your samples in the next part of the submission.
• Experiment description: Provide a description of the design and aims of your experiment in the 'Experiment description' section.
• Date for public release: Enter the date on which your data should be made public. If you do not have a definite release date then enter an estimate - you will be able to change the release date later if necessary.
• Publication: Provide any publication details here.

Once you have entered the Experimental design information click the 'Submit' button.

More Information Section

The two links in this section of the page will take you to forms where you can submit information quality control measures taken and any other additional qualifiers.

Quality Related Indicators (optional)

Describe measures taken to ensure or measure quality (e.g. biological replicates, dye swaps).

Once you have completed this section, click the 'Submit' button and return to the Experimental design page.

Additional qualifiers (optional)

These free text boxes allow you to describe any further information about an experiment design, or sample, that is not provided elsewhere.
Specify the name of the qualifier, the value (with appropriate unit) and the source of the value or any other information that help to define it, then click 'Submit'.
You can add more qualifiers by clicking the 'Create New' button or remove them by clicking the 'Remove' button.
Use the navigation links to move between the qualifiers.

Once you have entered all the additional qualifiers return to the Experiment design page.

Add Samples

Select the number of samples used in the experiment from the drop down list. If you have more than 10 samples, select 10+ from the list then specify the number in the text box provided

Click 'Create' and the specified number of samples will be listed in the 'Samples' section at the bottom of the page.
You can add more samples at any time by repeating this process.

Samples

Automatically created sample names will be shown here, you can edit these names in the next step.
To remove samples from the list, select them and click the 'Remove' button.

Sample descriptions

Select a sample from the Experiment design page and click 'View/Edit'. This will take you to the 'Sample description' page where you can provide information about the sample.

You must complete a sample description form for each sample used in your experiment.

• Sample name: Give your samples meaningful names. These names will be used throughout the submission.
• Sample details: Complete all the fields that are relevant to your sample.
• Experimental factor values: You must provide values for experimental factors. For reference samples you must still provide factor values, for example, time=0, genotype=wild type, etc.
• Protocols: Link the sample to a growth and treatment protocol (if relevant).

Remember to click the 'Submit' button to save your changes.
You can save time by using the 'Copy across sample description' feature (see below) to repeat the same information for several samples. Sample names and factor values will not be copied.
Use First, Previous, Next and Last links to move between sample descriptions.

Additional qualifiers

Additional qualifiers can be used to supply further information which has not been provided elsewhere, e.g. Qualifier: Sampling Site, Value: Tyne, Source: River from which sample was taken.

NOTE - If you choose to use additional qualifiers they must be entered for each sample, as they will not be copied by the 'Copy across sample description' feature.

Copy across sample description

Once you have provided the details for one sample and submitted the information, you can copy them to other samples.
To copy the information to all created samples:

• Click the 'Paste this sample description across all samples' button.

• Click the 'Copy contents of this sample description' button at the bottom of the sample description page (you will remain on the same sample description page).
• Navigate to the sample description page that you want to fill in.
• Click the 'Paste existing sample description' button at the top of the form.

Create Extracts

When you have completed all the sample descriptions click the 'Extracts (create/view/edit)' link, at the bottom of any sample description page, to go to the Create Extracts page.

To add new extracts

Select the number of extracts used in the experiment from the drop down list. If you have more than 10 extracts, select 10+ from the list then specify the number in the text box provided.

Click 'Create' and the specified number of extracts will be listed in the 'Extracts' section at the bottom of the page.

You can add more extracts at any time by repeating this process.

Extracts

The IDs of each extract related to the experiment are shown here.

Link each extract to the sample(s) they were created from by highlighting them in the sample ID boxes.

If this extract is a pool, simply link TWO or MORE samples to ONE extract and specify details in the 'Pooling protocol' (to be submitted in the 'Extract' page).
Click the 'Submit' button to save these links.

To remove extracts from the list, select the extract(s) and click the 'Remove' button.

The FIRST time you link each extract to a sample an extract name will be generated based on the sample name. This name will NOT be automatically updated if you make changes to the sample names or sample-extract links.

To change the automatically generated names, and link to the relevant protocols, select the extract and click 'View/Edit'. This will take you to the 'Extract' pages.

Extracts

You must complete an 'Extract' form for each extract used in your experiment. Here you can change the extract name, provide the extraction and pooling protocols, and create labeled extracts.

• Protocols: Link the extract to an existing extraction protocol by selecting it from the list provided, or create a new one.
  Link to a pooling protocol only if pooling was performed.

Remember to click the 'Submit' button to save your changes.
You can save time by using the 'Paste this extract description across all extracts' feature.
Use First, Previous, Next and Last links to move between extracts.

Create labeled extracts from each extract

Select the number of labeled extracts created from this specific extract from the drop down list.
Click 'Create' and the specified number of labeled extracts will be listed in the 'Labeled Extracts' section at the bottom of the page.
You can add more labeled extracts at any time by repeating this process.
Tip for Affy/single channel submissions - work through the extracts and create all the labeled extracts THEN edit the labeled extracts. This way you can use the 'Paste across all labeled extracts in experiment' feature to save time.

Labeled Extracts

The names of each labeled extract related to this specific extract are shown here.
To remove labeled extracts from the list, select the labeled extract(s) and click the 'Remove' button.

To change the automatically generated IDs, and link to the relevant protocols, select the labeled extract and click 'View/edit'. This will take you to the 'Labeled Extract' pages.

Labeled Extracts

You must complete a labeled extract form for each labeled extract used in your experiment. On this page you can change the labeled extract name, provide the labeling protocol and select the label used.

• Protocols: Link the labeled extract to an existing labeling protocol by selecting it from the list provided, or create a new one.
• Label used: Select the dye used to label this labeled extract.

Remember to click the 'Submit' button to save your changes
You can save time by using the 'Paste across...' feature. (NOTE - you can chose to paste the information across all labeled extracts created from the current extract, or across all labeled extracts created in the experiment)
Use First, Previous, Next and Last links to move between labeled extracts created from the same extract.

To hybridizations

Once you have completed the labeled extract descriptions for all the extracts in your experiment, click the 'To hybridizations' button to proceed to the 'Create Hybridizations' page.

To add new hybridizations

Select the number of hybridizations performed in the experiment from the drop down list. If you have more than 10 hybs, select 10+ from the list then specify the number in the text box provided.

Click 'Create' and the specified number of hybridizations will be listed in the 'Hybridizations' section below.
You can add more hybs at any time by repeating this process.

Hybridizations related to experiment

Select the array and labeled extracts which were used in each hyb. Your array design must have been submitted to show up in the drop down list.
If you used a commercial array design that is missing from this list please . If you used a custom array design you need to return to the 'Submission Types' page and make an array design submission.

Link each hyb to the array by selecting it from the 'array design name' drop down list.
Enter the batch number and serial number of the individual array used if applicable.
Select the labeled extracts used in each hyb from the drop down lists provided.
Click the 'Submit' button to save these changes.
To remove hybridizations from the list, select the hybridization(s) and click the 'Remove' button.

To change the automatically generated IDs, link to the relevant protocols, and upload the data files generated by each hyb, select the hybridization and click 'Upload data files'. This will take you to the 'Hybridization' pages.

Hybridization

You must complete a hybridization form for each hybridization in the experiment and upload the data files produced.

• Raw data: Submit the raw data files generated after scanning each array. If you are an Affymetrix user submit the .CEL file here (and .EXP if available). For all other submissions the raw data must be a single .txt or .gpr file.

• Normalized data: Submit data files created by normalization of your raw data if available. If you are an Affymetrix user you can submit the .CHP file here - if you did not use .CHP files in your analysis then you can submit data from some other software (e.g. dChip, RMA) in the final step of the submission. For non-Affy submissions the normalized data must be a single .txt file.

For more information on the format of the raw and normalized data files see the data file help page.

If you have problems uploading very large files then contact us at .

• Protocols: Link each hybridization to a hybridization and scanning protocol. If you have uploaded normalized data you will need to link to a normalization protocol.

Remember to click the 'Submit' button to save your changes
You can save time by using the 'Paste this hybridization description across all hybridizations' feature.
Use First, Previous, Next and Last links to move between hybridizations.

Once you have completed the hybridization descriptions for all the hybridizations in your experiment, return to the 'Create Hybridizations' page to continue to the final step.

Complete submission

• Combined data file: If you have generated a data file combining information from all your hybridizations you can upload it here.
  For information on how to format this file, see the data file help page.
• Transformation protocol: If you have supplied a combined data file, link it to an existing transformation protocol by selecting it from the list provided, or create a new one.

Finally, click the 'Complete submission' button.

What happens next?

Please see the general MIAMExpress help page for details:
What happens after MIAMExpress submission >>

Any further questions, please see our FAQ.