MAGE-TAB logo Submitting MAGE-TAB to ArrayExpress

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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:

Preparing your submission

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:

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Supported data file types

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:

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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The MAGE-TAB submissions system

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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After completing your experiment submission

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Tips on creating a MAGE-TAB spreadsheet

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:

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

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

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Real-world Examples

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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Last modified: Tue Feb 26 14:12:35 GMT 2008