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    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

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    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    • Legacy Projects
    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    screencap long reads webinar_ Metagenome Program
    Utilizing long-read sequencing for metagenomics and DNA modification detection webinar
    Watch the webinar on how the JGI employs single-molecule, long-read DNA sequences to aid with genome assembly and transcriptome analysis of microbial, fungal, and plant research projects.

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    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

    Read more

    martin-adams-unsplash
    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

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    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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User Programs
Home › User Programs › User Support › Project Management FAQ

Project Management FAQ

  1. Who is my project manager?
  2. What are the product catalog sequencing types that the JGI offers?
  3. How do I submit a proposal for sequencing or DNA synthesis?
  4. Who signs the User Agreement?
  5. How do I obtain a JGI login?
  6. I have new contact information. How can I update my JGI account?
  7. What are the guidelines for sample submission?
  8. Does the JGI recommended any specific protocols for sample preparation?
  9. I am an investigator located outside of the United States. How should I prepare my materials for shipment to the JGI?
  10. Can I request a culture/slant/DNA of an organism that has been sequenced at the JGI?
  11. How do I check the current status of a project?
  12. Where can I view the analysis and annotation for a project? How should I cite the analysis resources?
  13. What is the JGI data release policy?
  14. What authors should I include in my publications?
  15. How do I acknowledge the JGI for the sequencing or DNA synthesis work done for my project?
  16. 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

PMO Team

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?

The majority of JGI projects come from the user community. Find out about JGI’s calls for proposals, and submit your proposal online using the Work Initiation Process (WIP) interface.

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?

  1. Go to the “edit contacts” page.
  2. Use the form to update all information except email address.
  3. 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.

  1. 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.
  2. The Sample report lists sample-level metadata such as sample IDs and names, QC results, SRA accessions, library names, and protocol and platform details.
  3. 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

  • Microbial (IMG–ER)
  • Metagenome and Single Cell (IMG/ M-ER)
  • Fungal (Mycocosm)
  • Algal (Phycocosm)

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

 

  • Institutional User Agreements
  • Sequencing Sample Overview
  • Sequence Submission Requirements - DNA Synthesis Program
  • Project Management Office (PMO)
  • Project Management FAQ
  • Policies
  • Protocols

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