MSK Library Guides: Depositing Data in Repositories: GEO

How to submit to GEO

GEO is an open-access archive of high-throughput functional genomic data, including all array-based applications and some high-throughput sequencing data. Its features are designed around the common features of most of the technologies and instruments for producing this data in use today, and is constantly evolving to meet changing needs. If you have questions about whether your data is appropriate for submission to GEO, you can contact the repository with questions.

GEO submissions may remain private until a manuscript citing the data is published. Regardless of public status, accession numbers are assigned at most 5 days after submission via email. If you are submitting human data, it is your responsibility to ensure compliance with the Human Subject Guidelines.

Submitting high-throughput sequence data to GEO

Steps for submission:

Check that GEO accepts your data type.
Gather raw files.
Gather processed data files.
Download metadata spreadsheet and fill in Metadata tab for your study. Use one spreadsheet per data type (e.g., ChIP-seq, RNA-seq).
In the metadata spreadsheet file, list the MD5 checksum for all raw and processed data files in the 'MD5 Checksums' tab.
Create single folder on your computer that contains all raw and processed data files for your experiment. If you have multiple data types, please use one folder per experiment.
Transfer your data to GEO by FTP using these instructions.
After FTP transfer has completed, submit metadata file(s) on the Submit to GEO page.

Download required spreadsheets:

Video tutorials

GEO provides the following video tutorial to assist with submission:

How To Submit High-Throughput Sequence Data to GEO

Submitting microarray and other non-HTS data types to GEO

Non-HTS data submissions are made through GEOarchive. A GEOarchive submission consists of the following parts:

Metadata spreadsheet: this spreadsheet will contain descriptive information about your files and experiments. You must use the appropriate template for the microarray you used. You can read more information and download the templates at the below links
- Vendor specific templates
- Generic microarray templates corresponding to platforms already deposited in GEO
- Generic microarray templates corresponding to platforms not already deposited in GEO
- Platform-only template
  - Platform-only template
- Non micro-array data templates
  - Generic single channel submission template
  - Generic single channel submission template, including Platform
Matrix table: this spreadsheet will contain the final, normalized values that are comparable across rows and Samples, and preferably processed as described in any accompanying manuscript
Raw data files: provided as an accompaniment to your processed data to allow for unambiguous interpretation of your data
Platform: you can use the FIND PLATFORM tool to see if your platform has already been uploaded to GEO and assigned an accession number. If it has not, include the platform-only template linked above in your metadata sheet, and platform annotation columns in your matrix sheet.

Once you have collected the above documents, bundle all parts (Excel file containing the metadata spreadsheet and matrix spreadsheet, raw data files) together into a .zip, .rar, or .tar archive using a program like WinZip. There are two options to transfer the resulting archive to GEO:

Use the web form to Submit microarray or additional files to GEO.
Use FTP for large submissions, see detailed instructions here.