On this page: Introduction Preparing your submission Supported data file types The MAGE-TAB submissions system After completing your experiment submission Tips on creating a MAGE-TAB spreadsheet Example MAGE-TAB documents See also: Constructing a MAGE-TAB document, including: IDF detail SDRF detail Supported data file formats

MAGE-TAB is a new data format, designed by members of the microarray community as a simplified standard representation format for microarray data. MAGE-TAB documents can be used to provide experimental annotations for data submissions to the ArrayExpress repository database. MAGE-TAB is a tabular format, easily edited in any spreadsheet-based application (e.g., Microsoft Excel). The format is designed to be able to describe the most common experimental designs, including annotation required by the MIAME standard. MAGE-TAB is suitable for submitting both single-channel (e.g. Affymetrix) and two-channel data. It is somewhat related to the older Tab2MAGE format, but allows for much greater flexibility in describing microarray investigations.

A typical MAGE-TAB document consists of two parts, the IDF and the SDRF. The IDF contains overall information about the investigation, including the title, description, publication and contact details. It also contains information on the protocols used. The SDRF component describes the links between each sample step and the data acquisition and analysis steps, linking each ultimately to the data files.

MAGE-TAB can be used to submit microarray data to ArrayExpress in one of two ways. For most users, we recommend using our online MAGE-TAB submission system to create a template document, which should then be filled in by the user and uploaded to our web site alongside their data files.

For advanced users who wish to generate MAGE-ML from their MAGE-TAB documents, we provide a set of downloadable scripts to help with document conversion:

• MAGE-TAB to MAGE-ML
• Tab2MAGE to MAGE-TAB
• Tab2MAGE to MAGE-ML

Our MAGE-TAB submissions page is here: ArrayExpress MAGE-TAB submissions.

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

To submit data using MAGE-TAB you will need to provide the following information:

• Protocols describing your sample growth/treatment and processing steps.
• The ArrayExpress accession number of the array design (platform) used - more information on array designs here.
• A description of your experiment.
• Details of all the samples used in your experiment.
• Raw data files (e.g. .CEL, .gpr, .txt) for each hybridization you performed.
• Per-hyb normalized data and/or a Data Matrix file (submission of processed data is required for full MIAME compliance, but we will still accept your submission if this is not available).

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This table shows which files you can submit using MAGE-TAB. Do not edit your raw data files. There are definitions and more information on how to format normalized and combined data here:

• Supported raw data file formats
• MAGE-TAB Data Matrix format

Technology	Data type	File format	Quantity
Affymetrix	Raw	CEL plus EXP	1 CEL per hybridization - REQUIRED* 1 EXP per hybridization - optional
	Normalized	CHP and/or .txt	1 or more CHP and/or .txt per hybridization
	Combined "Data Matrix" file	.txt	1 or more .txt per experiment
Other	Raw	.gpr or .txt	1 or more .gpr or .txt per hybridization - REQUIRED*
	Normalized	.txt	1 or more .txt per hybridization
	Combined "Data Matrix" file	.txt	1 or more .txt per experiment

* Raw files are required for MIAME compliance, but if you really cannot provide them and you have processed data instead, then we can still accept the MAGE-TAB submission.

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Once you have finished preparing your MAGE-TAB document, please upload it with your data files to the ArrayExpress MAGE-TAB submissions website.

To submit data using this website:

1. Login or create a new user account if this is your first MAGE-TAB submission (note - previous Tab2MAGE submitters may re-use their old account).
2. Click 'Create experiment' to start your submission.
3. Enter your experiment name. If you want to generate a template spreadsheet then select one or more terms from each of the lists provided to describe your experiment (optional). Click 'Save experiment'.
4. Click 'Generate template' if you want to use the template (optional).
5. Click 'Upload files' then upload your completed spreadsheet and one or more zipped archives containing all your data files. If you are using separate IDF and SDRF documents, include your SDRF file in your zipped data file archive.
6. Click 'Submit experiment' to send this submission to us for curation.

If you have any questions please email the curation team at . If you are emailing about a specific submission tell us your username and experiment name in the email.

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• You will receive a immediate confirmation email from the MAGE-TAB submission system saying that your experiment has been submitted.
• Your submission will be put into curation status and 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 email you with any questions.
• We will send you an accession number when all the required information has been provided.
• We will load your experiment into ArrayExpress and provide you with a reviewer login for viewing the data before it is made public.
• To check the status of your experiment submission email us at . and remember to include your username and experiment name so that we can identify your submission.

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In most cases the MAGE-TAB document templates generated by our MAGE-TAB submissions website should help to get you started. To create a template you will need to create a new user account and start a new experiment submission. The system then asks you for a few basic details concerning your experiment and generates a template document which you can download and edit on your computer. If you have submitted MAGE-TAB to us before you can skip these steps and re-use your old template.

In some cases our standard templates may be too simple to capture all the detail of your experiment. To describe experiments which do not fit into our templates, the full expressivity of MAGE-TAB can be used instead. Please see these MAGE-TAB help notes for further information on what is possible with MAGE-TAB, or read the MAGE-TAB specification document. It is hoped that our template generation system will suffice for most users.

Here are some general tips on submitting MAGE-TAB documents to ArrayExpress:

• The templates generated by our system combine the IDF and SDRF components into a single document, to further simplify the process of submitting your data. If you prefer to create separate IDF and SDRF documents, these can also be uploaded to the submission web site.
• In the 'Experiment Description' part of the IDF section please clearly explain what you did in your experiment - this will help the curation team to check and process your spreadsheet.
• Enter an estimated release date in the 'Public Release Date' part of the IDF section. We will set your data to be made public on this date but you can ask us to change this later.
• When describing your protocols in the IDF section, give each of your protocols a unique identifier in the 'Protocol Name' row, e.g. 'My protocol 1'. Use these names in the SDRF section to refer to the relevant protocols.
• You may re-use previously submitted protocols by entering their accession numbers directly into the 'Protocol Name' IDF row. You may retrieve these accessions using the ArrayExpress web page. If your protocols have not yet been loaded into ArrayExpress, please contact the to obtain the accession numbers.
• The SDRF section is a table containing all the information about the samples you used and the hybridizations you performed. It must include the names of the data files that were produced for each hybridization.
• For most two-channel experiments the SDRF section will contain two lines for each hybridization to represent the two channels. Single-channel experiments usually have one line per hybridization.
• The number of 'Characteristics' columns in the SDRF section will depend on how much information you have about each of your samples. If you are using a template spreadsheet some suggested columns will be included but you can add or remove 'Characteristics' and 'Factor Value' columns as required.

For further help with MAGE-TAB document preparation, including the definitions of all the available fields, please see the following pages:

• MAGE-TAB overview
• IDF detail
• SDRF detail

For further help with MAGE-TAB submissions to ArrayExpress, please contact the

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Below is a selection of some of the real-world curated MAGE-TAB documents, created from Tab2MAGE spreadsheets submitted to ArrayExpress over the past few months:

IDF	SDRF	Experiment name	Platform	Link to experiment
E-TABM-16.idf	E-TABM-16_sdrf.txt	FDA-CDER MTS RNA reagent cross platform test	Multiple platforms	ArrayExpress
E-TABM-18.idf	E-TABM-18_sdrf.txt	Transcription profiling of 35 different Arabidopsis thaliana ecotypes	Affymetrix	ArrayExpress
E-TABM-22.idf	E-TABM-22_sdrf.txt	Transcription profiling of human lung cancers and lung cancer cell lines miRNA expression	One-channel custom array	ArrayExpress
E-TABM-33.idf	E-TABM-33_sdrf.txt	Transcription profiling of zebrafish development	Affymetrix	ArrayExpress
E-TABM-35.idf	E-TABM-35_sdrf.txt	Comparative genomic hybridization of 25 Coxiella burnetii isolates relative to the Nine Mile (RSA493) reference isolate	Affymetrix	ArrayExpress
E-TABM-54.idf	E-TABM-54_sdrf.txt	Comparative genome hybridization of 137 Bordetella pertussis strains	Two-color custom array	ArrayExpress
E-TABM-66.idf	E-TABM-66_sdrf.txt	Transcription profiling of normal and malignant human breast epithelial cells	Multiple platforms	ArrayExpress
E-TABM-70.idf	E-TABM-70_sdrf.txt	Transcription profiling of human cell lines treated with cytochalasin D and nocodazole with the aim of characterising tetraploid clones	Agilent	ArrayExpress
E-TABM-102.idf	E-TABM-102_sdrf.txt	Transcription profiling of wild type and ATF3 -/-mouse bone marrow macrophages stimulated with lipopolysaccharide over time	Affymetrix	ArrayExpress
E-TABM-134.idf	E-TABM-134_sdrf.txt	WGA-LCM and Genomewide Survey of Lung Cancer	Affymetrix	ArrayExpress
E-TABM-136.idf	E-TABM-136_sdrf.txt	Transcription profiling of human and chimpanzee heart, brain, testis and lymphblastoid cell lines to study functionality of intergenic transcription	Affymetrix	ArrayExpress
E-TABM-140.idf	E-TABM-140_sdrf.txt	Chromatin immunoprecipitation (ChIP-chip) of human erythroleukemia cell line K-562 with anti-histone antibodies using an ENCODE array	Two-color custom array	ArrayExpress
E-TABM-163.idf	E-TABM-163_sdrf.txt	Transcription profiling of murine presomitic mesoderms of 17 samples at various time points to identify cyclic genes of the mouse segmentation clock	Affymetrix	ArrayExpress
E-MEXP-880.idf	E-MEXP-880_sdrf.txt	Methylation profiling of normal and cancerous breast cells from human patients and cell lines in a 125 kB region of the HOXA cluster	Two-color custom array	ArrayExpress
solexa_example.idf	solexa_example.sdrf.txt	Example MAGE-TAB documents for a hypothetical high-throughput sequencing submission (e.g. Solexa, 454)	Solexa	Not available

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