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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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    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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    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 › Sequencing Sample Overview

Sequencing Sample Overview

This document contains a brief description of the process needed to prepare and ship samples for sequencing by the JGI.  Additionally it includes instructions on accessing sample-level reports and track statuses.  Please follow the steps outlined below. If you have any questions, please contact your Project Manager or jgi-project_management@lbl.gov.

DNA and RNA Sample Preparation

1) Review JGI sample QC requirements and protocols

Obtaining DNA and RNA of suitable quantity and quality has been the rate-limiting step for many projects at the JGI. The quality of the starting material is one of the greatest predictors of a successful sequencing project. It is imperative that users properly assess DNA or RNA mass prior to shipment to the  JGI. The documents below (posted with permission) demonstrate the importance of proper nucleic acid quantification in our Illumina and PacBio sequencing workflows and provide guidance as to how to perform sample QC prior to shipment:

  • Importance of Sample QC
  • Sample Quality and Contamination
  • Genomic DNA Sample QC Protocol
  • Total RNA Sample QC Protocol
  • Small RNA Sample QC Protocol

2) Review guidelines detailing quantity and quality requirements

Please review the appropriate guidelines detailing the quantity & quality requirements for samples submitted to the DOE JGI.

  • Plate-based Preparation Guidelines
  • DNA Preparation Guidelines
  • RNA Preparation Guidelines
  • GenTegra DNA Preparation Procedure
  • GenTegra RNA Preparation Procedure
  • DNAstable Plus Preparation Procedure
  • RNAstable RNA Preparation Procedure

Note: the manufacturer of DNAstable and RNAstable has discontinued these products and they are available in very limited supply.  JGI will continue to accept samples in this format.

Sample Shipping

1) Complete Sample Metadata form

Sample metadata is collected via spreadsheet or directly via a web interface prior to shipping samples to the JGI.

  1. PI sends Project Manager (PM) a list of organism names (or for metagenomes, sample names).  Need help naming your organisms?  See our Taxonomy Quick Guide.
  2. PM sends PI the sample metadata spreadsheet to fill out (or provides a link to complete the form online)
  3. PI completes and returns the spreadsheet to the PM (or completes the form online)
  4. PM submits metadata to JGI database for shipping approval (n/a if using web-based form)

All shipments originating outside the United States must also include a completed Export Certification Form.

2) Obtain Approval for Shipping

Before approval to ship is granted, you must have completed submission of all project metadata for all project materials.  PI will receive a shipping approval email with shipping instructions.  Provide your shipping address to receive barcoded tubes/plates that should be used to ship your samples to the JGI.   Samples that have not been approved to ship or are not sent in JGI-supplied tubes/plates will be returned to the user. 

PLEASE NOTE: The JGI will not accept any materials classified above NIH Biosafety Level 2.

3) Review Shipping Instructions

After receiving shipping approval and your barcoded tubes/plates, please refer to the emailed instructions for shipping your materials to the JGI. The Shipping Checklist below will assist you in verifying that all required information is included. Please retain your carrier’s tracking information.

  • JGI Shipping Checklist
  • International Shipments (For shipping packages internationally — including Canada! — please use these instructions.)
  • TSCA Form for International Shipments

4) Shipping your samples

Send your package on a Monday or Tuesday of the week specified in the shipping approval email (please avoid U.S. federal holidays). We recommend shipping your samples on dry ice.  Please contact your project manager for alternate solutions.

Sample Tracking and Status Reports

The PI will receive an automated email once the samples are received and checked into our freezer.  Your project manager will keep you updated as your samples move through QC and into the library and sequencing pipelines.  You will receive automated emails as raw sequence data becomes available, and as analysis is completed.

You can view the status of your projects at any time by accessing various reports on the JGI Portal.  Use the search feature to bring up a list of projects that you are interested in, then click 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.

We look forward to getting your project started!

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

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