- Who is my project manager?
- What are the product catalog sequencing types that the JGI offers?
- How do I submit a proposal for sequencing or DNA synthesis?
- Who signs the User Agreement?
- How do I obtain a JGI login?
- I have new contact information. How can I update my JGI account?
- What are the guidelines for sample submission?
- Does the JGI recommended any specific protocols for sample preparation?
- I am an investigator located outside of the United States. How should I prepare my materials for shipment to the JGI?
- Can I request a culture/slant/DNA of an organism that has been sequenced at the JGI?
- How do I check the current status of a project?
- Where can I view the analysis and annotation for a project? How should I cite the analysis resources?
- What is the JGI data release policy?
- What authors should I include in my publications?
- How do I acknowledge the JGI for the sequencing or DNA synthesis work done for my project?
- What JGI-sponsored meetings or workshops are available to me?
1. Who is my project manager?
- Eukaryotic projects: Kerrie Barry, Vivian Ng
- Prokaryotic projects: Nicole Shapiro, Tijana Glavina del Rio, Miranda Harmon-Smith
- DNA Synthesis: Miranda Harmon-Smith
- Special Projects: Christa Pennacchio
2. What types of products does the JGI offer?
The JGI offers multiple product offerings for each program.
3. How do I submit a proposal for sequencing or DNA synthesis?
4. Who signs the User Agreement?
The “User” signing the JGI User Agreement will be an authorized representative from your institution (usually a legal counsel representative) . The User Agreement and corresponding Appendix must be signed and returned before work on your proposal may begin. You will be notified by your project manager in the initial correspondence with you if the User Agreement and Appendix are active and if no additional signatures are required.
5. How do I obtain a JGI login?
You can request a JGI Single Sign On account at https://signon.jgi.doe.gov. This account can be used to submit proposals, Sample and Project metadata and to access JGI tools and systems.
6. I have new contact information. How can I update my JGI account?
- Go to the “edit contacts” page.
- Use the form to update all information except email address.
- To update your email address, click the “Request email change” link. This will generate an email that will go to an administrator to complete the process.
7. What are the guidelines for sample submission?
Guidelines detailing the quantity and quality requirements for samples submitted to the JGI can be found here. Please inform your project manager of an accurate date of sample preparation and anticipated shipment. Based on that date, the project manager may then schedule and allocate resources for DNA sequencing.
8. Does the JGI recommend any specific protocols for sample preparation?
No. However, the JGI does maintain a list of protocols used successfully by investigators in the past. These protocols are not endorsed by and have not been validated by the JGI, but are provided as general guidance.
9. I am an investigator located outside of the United States. How should I prepare my materials for shipment to the JGI?
Guidance on international shipments can be found in the “sample shipping” section of the Sequencing Sample Overview webpage.
Note: the JGI does not recommend shipping a dry/lyophilized pellet. It is usually very difficult to resuspend the pellet once it is received. If you have concerns about shipping your DNA/RNA on dry ice, DNAstable or RNAstable may be appropriate alternatives (Jan 2021 note: the manufacturer of DNAstable and RNAstable has discontinued these products and they are available in very limited supply). Please discuss with your project manager.
10. Can I request a culture/slant/DNA of an organism that has been sequenced at the JGI?
The JGI does not maintain DNA, cultures or stocks of any organisms. These materials should be obtained by contacting the collaborator listed on the “info” page for that organism on the Genome Portal.
11. How do I check the current status of a project?
You can view the status of all public projects on the JGI Genome Portal.
The PI and all authorized users can also generate various reports. Access the reports by searching for projects in the portal search page and then clicking the blue “reports” button on the right side.
- The Project Overview report includes project-level metadata such as the project name, current status, NCBI & JGI taxonomy, and data locations on the various JGI Portals.
- The Sample report lists sample-level metadata such as sample IDs and names, QC results, SRA accessions, library names, and protocol and platform details.
- The Sample QC report lists all the samples received for a project, metadata about the samples, and the sample QC results.
12. Where can I view the analysis and annotation for a project? How can I add to an existing annotation? How should I cite these resources in my publication?
Analysis and annotation of publicly available projects can be accessed via the Genome Portal, at the following sites:
- Microbes: IMG (citation: https://doi.org/10.1093/nar/gkaa939)
- Metagenomes and Single Cells: IMG/M (citation: https://doi.org/10.1093/nar/gkaa939
- Fungi: Mycocosm (citation: https://doi.org/10.1093/nar/gkt1183)
- Algae: Phycocosm (citation: https://doi.org/10.1093/nar/gkaa898)
- Plants: Phytozome (citation: https://doi.org/10.1093/nar/gkr944)
The following tools are available for functional annotation/curation of your genomes
13. What is the JGI data release policy?
In general, data generated by the JGI are immediately released to the public via JGI portals and NCBI. Read More about our Policies.
14. What authors should I include in my publications?
Individuals who materially contribute to publishable work must be included as authors. Your project manager can provide you with contact information and institutional affiliations for individuals associated with your proposal. The JGI Publication Policy outlines additional information related to publication.
15. How do I acknowledge the JGI for the sequencing or synthesis work done for my project?
The JGI asks that you please use the JGI Auspice Statement to acknowledge the sequencing done by the JGI.
16. What JGI-sponsored meetings or workshops are available to me?
- Five-day Microbial Genomics and Metagenomics workshops are offered each year.
- Annual DOE JGI User Meeting
- Other events