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 tracking statuses. Please follow the steps outlined below. If you have any questions, please contact your Project Manager or email@example.com.
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:
- JGI’s Genomic DNA Sample QC Protocol
- JGI’s Total RNA Sample QC Protocol
- JGI’s Small RNA Sample QC Protocol
- DNA Extraction 101 – tips, kits, and protocols (from PacBio)
- Guidance for sample collection and storage (from PacBio)
- Best practices for High Molecular Weight DNA extraction and quality control (from PacBio)
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.
- 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.
1) Complete Sample Metadata form
Sample metadata is collected via spreadsheet or directly via a web interface prior to shipping samples to the JGI.
- 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.
- PM sends PI the sample metadata spreadsheet to fill out (or provides a link to complete the form online)
- PI completes and returns the spreadsheet to the PM (or completes the form online)
- 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!