Copying data to GEO

Who is this guide for?

This guide is for Basepair users who are ready to copy their data to GEO. Basepair's solution to that is the "Copy data to GEO" pipeline. However, before and after you run that analysis you need to perform a couple, simple actions on your GEO account. If you do not have already have a GEO account, please go here: https://www.ncbi.nlm.nih.gov/account/?back_url=/geo/submitter/

Note: It used to be easier to upload data to GEO, but recent changes made it require a few extra steps. But do not worry, if you follow this guide it should be pretty easy.

Step-by-step guide

Step 1: Go to the GEO website

Once you have your GEO account setup, please go to the high-throughput sequencing data submission page: https://www.ncbi.nlm.nih.gov/geo/info/seq.html

Scroll down and click on the "Transfer files" button. See the screenshot below.

Step 2: Create your GEO personal directory

Once clicked, you will be brought to another page. Click on the "Create personalized upload space" button. Again, see the screenshot below:

Step 3: get your GEO personal directory

After a few seconds (and you may need to refresh your browser), you should see more text on the webpage. You need to copy the text that is displayed after "Step 1: Your personalized upload space is: ". In the example screenshot below, you need to copy "uploads/[email protected]_NNNNNN".

Step 4: Start the "Copy to GEO" analysis

Once you have the text you copied from Step 3, you are ready to start the "Copy data to GEO" analysis. 

Step 5: Download and edit the metadata spreadsheet

Once the analysis is done, you need to download the metadata spreadsheet from here: 

https://www.ncbi.nlm.nih.gov/geo/info/examples/seq_template.xlsx

Fill in the template with project and biological information.

Next, you will need to download the output file from running the "Copy to GEO" analysis. It will be under the "Info" tab. Copy the data about files and checksums to the metadata spreadsheet you just filled out with information.

Step 6: Upload the metadata spreadsheet

Once the spreadsheet is filled out, you will need to upload it to the NCBI FTP directory. This is very easy to do. First, you will need to download a program called FileZilla from here: https://filezilla-project.org/  FileZilla is a popular and free tool.

Open the program and fill in the Host, Username, and Password fields like shown in the screenshot below. 

Host: ftp-private.ncbi.nlm.nih.gov

Username: geoftp

Password: rebUzyi1

Once filled out, click "Quickconnect". Once you are connected, fill in the "Remote site" input with your personalized GEO directory from step 3. However, be sure to prefix it with the "/" character.

Now you are ready to upload the spreadsheet. Your local computer's filesystem is displayed on the top left. Use it to navigate to where you have your spreadsheet. The files in your current selected directory will be shown on the bottom left. Once you located your spreadsheet, just double click it to upload. And that is it!

Step 7: Notify GEO

Once the spreadsheet is uploaded you will need to navigate back to the webpage shown in Step 3 and click on "Notify GEO" button.

Need more help?

If you need any further help, please do not hesitate to reach out to us using either the chat icon in the lower right hand corner of your screen or creating a ticket by sending an email to [email protected].