DOE Joint Genome Institute

  • COVID-19
  • About
  • Phones
  • Contacts
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    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.

    More

    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

    More

    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • 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.

    More:

    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.

    Read more

    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.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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.

    More

    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.

    More

    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.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
    • User Support
    • Submit a Proposal
    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

    Read more

    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

    Read more

    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Publications
    • Scientific Posters
    • Newsletter
    • Logos and Templates
    • Photos
    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 .

    More

    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.

    More

    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

    Read more

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
  • DNAstable Plus Preparation Procedure
  • RNAstable RNA Preparation Procedure

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 complete the Export Certification Form.  Email this to your Project Manager along with your sample metadata 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 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

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Podcasts
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • RSS feed
  • Flickr
  • LinkedIn
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2021 The Regents of the University of California