Tab2MAGE Spreadsheet Submission Guidelines
In this help page:
Overview
Tab2MAGE is a format for describing a microarray experiment in a spreadsheet. You can submit a Tab2MAGE spreadsheet to ArrayExpress, along with your data files, using our Tab2MAGE submission system. Tab2MAGE is suitable for submitting both single-channel (e.g. Affymetrix) and 2-channel data.
The Tab2MAGE submission system is here:
Tab2MAGE ArrayExpress submissions page >>
There is general information about ArrayExpress submissions, accession number assignment and data privacy here:
ArrayExpress submissions help page >>
To submit data using Tab2MAGE you'll 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 combined data file (for full MIAME compliance some sort of processed data is required but we will still accept your submission if this is not available)
Supported data file formats
This table shows what files you can submit using Tab2MAGE. 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 >>
*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 Tab2MAGE submission.
Tab2MAGE submission system
To submit a Tab2MAGE spreadsheet to ArrayExpress go to the Tab2MAGE submissions page:
Tab2MAGE ArrayExpress submissions page >>
- Login or create a new user account if this is your first Tab2MAGE submission.
- Click 'Create experiment' to start a new experiment submission.
- 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'.
- Click 'Generate template' if you want to use the template (optional).
- Click 'Upload files' then upload your completed spreadsheet and all your data files in one or more zipped archives.
- Click 'Submit experiment' to send this submission to us for curation.
After completing your experiment submission:
- You'll receive a immediate confirmation email from the Tab2MAGE 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.
Tips on creating a Tab2MAGE spreadsheet
Full instructions on how to complete a Tab2MAGE spreadsheet are here:
These are some general points:
- You can create your own Tab2MAGE spreadsheet from scratch but you may find it quicker to use a template spreadsheet generated by the submission system, or start with a Tab2MAGE spreadsheet from a similar experiment. Have a look at the examples here: Example Tab2MAGE spreadsheets
- In the 'description' part of the 'Experiment 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 'release_date' part of the 'Experiment section'. We will set your data to be made public on this date but you can ask us to change this later.
- In the 'Protocol section' of the spreadsheet give each of your protocols a unique identifier in the 'accession' column, e.g. 'My protocol 1'. Use these identifiers in the 'Hybridization section' to refer to the relevant protocols.
- The 'Hybridization 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 2-channel experiments the 'Hybridization section' will contain 2 lines for each hybridization to represent the 2 channels. Single-channel experiments usually have 1 line per hybridization.
- The number of columns in the 'Hybridization 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 BioMaterialCharacteristics and FactorValue columns as required.
Definitions of column headings in the 'Hybridization section':
- BioSource - a biological starting material used in the study, e.g. a mouse, a tumor sample, a bacterial culture, a group of seedlings. Enter a unique name for each BioSource used and remember to give biological replicates different names e.g. 'patient 1 - tumor sample 1', 'treated culture A'.
- BioMaterialCharacteristics [category] - a characteristic of the BioSource. You can include as many of these columns as you need to describe your BioSources. Each column must have a different category in the column title, e.g. BioMaterialCharacteristics[Sex], and must contain the values for this category, e.g. male.
- Sample (optional) - a sample taken from a BioSource. Often a single Sample is taken from each BioSource so you can omit this column. The Sample column could be used if you took multiple samples from a single BioSource during a time series for example. If using the Sample column enter a unique name for each Sample, e.g. 'treated culture A - 0hours', 'treated culture A - 2hours'.
- Extract - the DNA, RNA or protein extracted from a Sample. Enter a unique name for each Extract used.
- Immunoprecipitate (optional) - for ChIP-chip experiments Tab2MAGE allows you to create Immunoprecipitates from Extracts. Enter a unique name for each immunoprecipitate created, e.g. 'culture A - mock', 'culture A - anti H3'.
- LabeledExtract - RNA, DNA or protein labeled with a particular dye such as biotin or Cy3. You can create multiple LabeledExtracts from the same Extract but remember to give them different names if they were labeled with different dyes, e.g. 'extract A cy3', 'extract A cy5'.
- Hybridization - a single array or chip which has one or two LabeledExtracts hybridized to it.
- Scan (optional) - a scan of an array. Usually a single Scan is taken for each Hybridization so you can omit this column. If multiple scans are taken then enter unique names for them, e.g. 'Hyb1 scan 500 PMT', 'Hyb 1 scan 700 PMT'.
- FactorValue [factor] - an experimental factor is a property which varies between samples and is important in the interpretation of your data. You need a separate FactorValue[factor] column for each factor in the experiment, e.g. FactorValue[Compound]. In each FactorValue column enter the value relevant to that particular sample, e.g. doxycycline.
- Protocol [type] - refer to the relevant protocol from your 'Protocol section' by entering the identifier from the protocol accession column. Several different types of protocol column are allowed such as Protocol[grow], Protocol[treat], Protocol[extract].
- File [type] - enter the EXACT name of the relevant data file (the casing, spacing and file extension must match the actual file names). Three types of file column are allowed: File[raw], File[normalized], File[transformed].
- Array [accession] - enter the ArrayExpress accession number of the array design used.
Any further questions, please see our FAQ.
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