Submitting data

GEO accepts many categories of high-throughput functional genomic data, including all array-based applications and some high-throughput sequencing data. This page summarizes deposit options and formats.

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 e-mail us at geo@ncbi.nlm.nih.gov with a brief description of the type of data you are trying to submit, and one of our curators will quickly get back to you.

Data types
- Array submissions
  - General
  - Affymetrix
  - Agilent
  - Nimblegen
  - Illumina
- RT-PCR submissions
- High-throughput sequence submissions
- Traditional SAGE submissions
Submission format options
Basic requirements for submissions
Fast facts about submitting data

Submission format options Back to top

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. Regardless of the deposit method you choose, your final GEO records will look the same and contain equivalent information.

GEOarchive

Recommended method for most submissions.
Quickly describe your study using Excel spreadsheet templates.
Complete instructions »

Submit

SOFT and MINiML formats

Good option if your data and metadata are already in a database, and you can generate and export data in SOFT plain text format or MINiML XML format.
Complete SOFT instructions »
Complete MINiML instructions »

Submit

All deposit options described above can be used for any data type. However, the majority of GEO submitters use common commercial arrays (Affymetrix, Agilent, Illumina or Nimblegen) each of which has unique properties and file types. It is recommended that submitters who use the 4 common commercial arrays see these recommendations:

Basic requirements for array submissions Back to top

Your final GEO records will look something as follows:

Schematic overview of GEO data submission.

For almost all array data submissions, you will be asked to provide the following information:

A	Text description of the array or sequencer
B	Text tab-delimited table of the array template
C	Text description of the biological sample and protocols to which it was subjected
D	Text tab-delimited table of processed hybridization result or sequence counts
E	Raw data file, or processed sequence data file
F	Text description of the overall experiment
G	Tar archive of raw data files, or processed sequence data files

Fast facts Back to top

All the deposit methods described above support MIAME-compliant data submissions. More...
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...
You can allow reviewers anonymous access to your private submissions. More...
GEO accession numbers are normally approved within 5 business days after completion of submission. If you do not receive an e-mail from us within 5 business days of your submission, please first check your spam or junk e-mail folders because some systems recognize GEO e-mail correspondence as spam, then e-mail us at geo@ncbi.nlm.nih.gov to inquire about your submission. More...
All the deposit methods described above support submission of many data types, including:
- Gene expression (see example)
- High throughput quantitative sequence data (see example) (see specific instructions)
- ChIP-chip (see example)
- ArrayCGH (Comparative Genomic Hybridization) (see example)
- SNP arrays (see example)
- SAGE (see example)
- Protein arrays (see example)
Human Genomic Data Submitted to Unrestricted-Access Repositories

NIH-funded studies: If you plan to submit large-scale human genomic data, as defined by the NIH Genomic Data Sharing (GDS) Policy, to be maintained in an unrestricted-access NCBI database, NIH expects you to 1) submit an Institutional Certification to assure that the data submission and expectations defined in the NIH GDS Policy have been met, 2) register the study in NCBI BioProject regardless of where the data will ultimately reside (e.g., GenBank, SRA, GEO). If you have any questions about whether your research is subject to the NIH GDS Policy, please contact the relevant NIH Program Official and/or the Genomic Program Administrator. If you plan to submit genomic data from human specimens that would not be considered large-scale, it is your responsibility to ensure that the submitted information does not compromise participant privacy and is in accord with the original consent in addition to all applicable laws, regulations, and institutional policies.

Non-NIH-funded studies: If your data are not NIH-funded, you are not required to comply with GDS policy but you must have the appropriate consent/permission to submit the data to a public database like GEO. GEO is not able to help interpret your consent forms, you should consult with your IRB on that. It is your responsibility to ensure that the submitted information does not compromise participant privacy and is in accord with the original consent in addition to all applicable laws, regulations, and institutional policies. If you do not have consent to make the data fully public in a database like GEO, you can apply to the NIH Office of Science Policy to find an NIH Institute that will sponsor your study in NCBI's dbGaP database. dbGaP has controlled access mechanisms and is an appropriate resource for hosting sensitive patient data. The sponsor would create a Data Access Request and Use Certification and define use restrictions for use in approving data access requests.
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...