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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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  • Our Projects
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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    • IMG
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    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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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 or Vivian Ng
  • Prokaryotic projects: Tijana Glavina del Rio, Danielle Graham, or 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 requesting sequencing, metabolomics 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, Gentegra products may be appropriate alternatives (see specific protocols on our sample guidelines page) and please discuss details 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 released to the public via JGI portals and the NCBI a year after generation.  Read More about our Policies.

14. What authors should I include in my publications?

Individuals who materially contribute to publishable work should 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-related meetings or workshops are available to me?

  • Five-day Microbial Genomics and Metagenomics workshops are offered each year.
  • IMG webinar series
  • Annual DOE JGI User Meeting
  • JGI webinars
  • KBase webinars
  • NMDC community conversations

 

  • 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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