How to submit data to NCBI GEO via HPC
Obtaining GEO Upload Information
1. Create a myNCBI account here
2. Obtain a personal upload directory from NCBI (this should come with a GEO File Transfer Protocol)
Gather Files for Submission
1. Download and fill in the GEO metadata spreadsheet
2. Gather all the raw data files and processed data files into one directory on HPC (transferring data to HPC)
3. Calculate the md5sum for all data files (md5sum examples)
4. Fill in the “checksum” cell with the calculated md5sum for each file
5. Once the Metadata spreadsheet is complete upload to HPC in the same directory as the data files
FTP to NCBI GEO
NOTE: Once you FTP in, the connection will timeout within 60 seconds of inactivity. When that happens, you just ‘exit’ and ftp again.
1. Navigate to the HPC directory containing all the files you want to upload
2. Then type ftp host address (example: ftp ftp-private.ncbi.nlm.nih.gov) (should be letter ‘e’ under Step 2 of the GEO File Transfer Protocol)
3. You will then be asked to enter the username and password for the FTP server (under host address, this is not your MyNCBI account info)
4. Type prompt n (turns off interactive mode)
5. Then navigate to your personal NCBI GEO upload directory (cd /upload/personaldirectory)
6. Make a directory for your new submission (mkdir geo_upload_example)
7. Navigate into that new directory
8. Type mput * (All the files in the HPC directory you were in will now get uploaded to your GEO submission directory)
9. All of your files should have been uploaded. You can check with ls.
10. Type exit to leave ftp
Notify NCBI of the Upload
1. After the FTP transfer is complete, notify GEO by clicking the “Notify GEO” button.
2. You will need to specify the new GEO submission directory you uploaded the files into.
Finished! You should receive your GEO Accession Code within 5 business days.
link to NCBI GEO Submission site for more information