Submitting data
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Deposit options
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The table below summarizes GEO deposit options and formats.
Deciding which method to
use depends on the amount of data you have to submit, the format in which your data currently exist, and what applications you are familiar with.
We aim to make data deposit procedures as straightforward as possible and will provide as much assistance as you require to get your data submitted to GEO.
If you have problems or questions about the submission procedures,
just email us at geo@ncbi.nlm.nih.gov and one of our curators will quickly get back to you.
| Option |
Format |
Key points |
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| Web deposit |
Web forms |
Deposit of individual records.
Simple step-by-step interactive Web forms.
Good if you have a small number of Samples to submit.
(Affymetrix users can deposit CEL and CHP files here, but if you use RMA or another program that generates value matrices, we recommend the GEOarchive batch deposit option instead).
Complete instructions... |
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| GEOarchive |
spreadsheets
(e.g., Excel) |
Batch deposit.
Good if you have many Samples to submit, and the normalized data for all
Samples are available in a single table or spreadsheet.
(Affymetrix submissions - CEL files, and CHP files or value matrices can be provided).
Complete instructions... |
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| SOFT |
plain text |
Batch deposit.
Good if you have many Samples to submit, or if your data are already in a database.
(Affymetrix submissions - CEL files, and CHP files or text tables can be provided).
Complete instructions... |
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| MINiML |
XML |
Batch deposit.
Use if you are familiar with XML and can generate MINiML formatted files.
Good if your data are already in a database, or if you have many Samples to submit.
Complete instructions... |
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Basic requirements
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Your final GEO records will look something as follows:
For almost all data submissions, you will be asked to provide the following information:
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Text description of your array |
Platform submission is not necessary if your array is already in GEO (e.g., Affymetrix chips).
In this case, all you need is a reference to the Platform accession number (GPLxxx).
Use the FIND PLATFORM tool to locate arrays.
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Text tab-delimited table of the array template |
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Text description of a biological sample |
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Text tab-delimited table of processed hybridization result
(may optionally include raw data columns) |
For Affymetrix data, a CHP file may be supplied instead of a tab-delimited table (but if you generate/analyze RMA or other non-CHP files,
we recommend providing those rather than CHP files). |
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Original raw data file |
External raw data files, e.g., Affymetrix .CEL files or GenePix GPR files. |
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Text description of the overall experiment |
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Fast facts
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| All the deposit methods described above support
MIAME-compliant data submissions. More information... |
| Regardless of the deposit method you choose, the final GEO records will look the same and contain equivalent information. |
| Your GEO submissions may remain private until a manuscript describing the data is published. More information...
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| You can allow reviewers access to your private submissions. More information...
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| GEO accession numbers are normally approved within 2-5 business days after completion of submission.
If you need approval of your GEO accession numbers to be expedited, e-mail us at geo@ncbi.nlm.nih.gov. More information... |
| All the deposit methods described above support submission of many data types, including:
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| You can update or edit your existing GEO records at any time using any of the formats described above, and regardless of the format in which they were originally uploaded.
More information... |
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