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| | 2 | == Submitting a sequencing dataset to GEO == |
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| | 4 | Almost every journal requires an experiments that include high-throughput sequencing to share the high-throughput sequence data on a repository like [[https://www.ncbi.nlm.nih.gov/geo/ | NCBI's GEO]]. |
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| | 6 | The best source of information for how to submit this data is NCBI's page for [[https://www.ncbi.nlm.nih.gov/geo/info/seq.html | Submitting high-throughput sequence data to GEO]]. |
| | 7 | BaRC can help prepare the files and perform the GEO submission or we can help you do it yourself. |
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| | 9 | The best ways to start is to [[https://www.ncbi.nlm.nih.gov/geo/info/examples/seq_template.xlsx | Download the metadata spreadsheet (template and examples)]] and start to fill out the description of your experiment and the samples that comprise it. Explain everything clearly enough so that people can understand an overview of your experiment from the GEO page, without having to read all of your publication. Spelling out words, avoiding acronyms, and using clear nomenclature will be a big help to others who might want to access your data. If BaRC is helping you with the file submission, they can fill out the bottom part of the spreadsheet. |
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| | 11 | You or BaRC will need to assemble all of your sequencing (fastq.gz) files and summary files (which will depend on the type of experiment). If some of your samples weren't analyzed for the publication, you'll want to decide whether you want to make them public or not. |
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| | 13 | If you ask BaRC for help with submitting sequencing or other files to NCBI GEO, |
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| | 15 | 1. Go to NCBI and log in: https://www.ncbi.nlm.nih.gov/account/ NCBI allows you to log in with a variety of types of accounts.[[br]] [[br]] |
| | 16 | 1. Go to the GEO submission page: https://www.ncbi.nlm.nih.gov/geo/submitter/ [[br]] [[br]] |
| | 17 | 1. Fill in information about you on the left. On the right side of the page, uncheck "Same as Investigator" and fill in the name and email of the BaRC person who is helping you.[[br]] [[br]] |
| | 18 | 1. Click the Save button.[[br]] [[br]] |
| | 19 | 1. Click the "New submission" button.[[br]] [[br]] |
| | 20 | 1. On the next page, click the "Submit high-throughput sequencing" link.[[br]] [[br]] |
| | 21 | 1. Click the "Transfer files" button.[[br]] [[br]] |
| | 22 | 1. Click the "Create personalized upload space" button.[[br]] [[br]] |
| | 23 | 1. Wait until you see the "Your personalized upload space is: " message. [[br]] [[br]] |
| | 24 | 1. Send this information to the BaRC person who is helping you.[[br]] [[br]] |
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| | 26 | After the BaRC person has finished uploading your data to GEO, they will let you know. |
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| | 28 | 1. Go back to GEO, log in, and go to https://submit.ncbi.nlm.nih.gov/geo/submission/ [[br]] [[br]] |
| | 29 | 1. Let NCBI know that your FTP file transfer to GEO is complete. [[br]] [[br]] |
| | 30 | 1. NCBI will let you and BaRC know when your private-for-now GEO web pages are available. [[br]] [[br]] |
| | 31 | 1. Check that the sample descriptions are clear and complete. [[br]] [[br]] |
| | 32 | 1. Right before or after your publication is made public, change the GEO access from private to public. [[br]] [[br]] |
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