Guidelines for submission of Genomic DNA to the DOE Joint Genome
Institute

> **The JGI has sequenced over 350 prokaryotic, eukaryotic and
> metagenomic projects and finished over 100 genomes. DNA quality
> (molecular weight and concentration) and quantity are two of the most
> critical components in the success of sequencing projects. If you
> cannot meet the JGI specifications for DNA or have questions or
> concerns, please contact jgi_project_management@lanl.gov and your
> project manager.**

**[JGI Starting Material Specifications: Quantity]{.underline}**

-   *75 -- 100 μg* of high molecular weight genomic DNA (HMW gDNA) for
    whole genome shotgun projects.

> Quantity of gDNA should be measured by agarose gel QC. Please refer to
> QC gel protocol: http://my.jgi.doe.gov/general/index.html
>
> Note: We realize these DNA quantities may not be possible for
> environmental samples, but the project will have the best chances for
> success if this amount can be sent. It is unlikely that a fosmid
> library can be constructed from less than 40 μg DNA, or that a
> short-insert (3 kb) library can be constructed from less than 10 μg.
> Whole genome amplification is NOT accepted.

**[JGI Starting Material Specifications: Quality]{.underline}**

-   *High molecular weight* -- The bulk of the eDNA prep should be
    larger than the 23KB lambda Hind III marker on an agarose gel. In
    order to construct a fosmid library the majority of the eDNA should
    be \~40kb.

-   The concentration of resuspended eDNA must be \>= 100 ng / μl as
    judged by agarose gel / mass markers. See "Quality control-gel
    electrophoresis conditions" below.

-   *Uncontaminated --* RNA blobs and discrete bands require clean-up.
    Please refer to recommended RNAse I clean-up protocol:
    http://my.jgi.doe.gov/general/index.html

**[JGI Starting Material Specifications: Shipping]{.underline}**

> *Prior to shipping samples to the JGI, the eDNA prep must first be
> reviewed & approved. Complete the appropriate RI (Step 3 in
> http://my.jgi.doe.gov/general/gettingstarted.html) and email it along
> with a well labeled gel image of your eDNA prep to your project
> manager. See the "Quality control-gel electrophoresis conditions" at
> the end of this document for detailed instructions on running the QC
> gel or find the complete JGI protocol:*
> http://my.jgi.doe.gov/general/index.html
>
> Format for shipping in order of preference:

-   Resuspended in TE (10 mM Tris, ph 7.5 -- 8, EDTA 0.1 mM) at \>= 100
    ng/ μl shipped on dry ice

-   Ethanol pellet shipped at RT or on wet ice. Note some ethanol
    pellets the JGI has received will not spin down and resuspend.

-   Dry pellet shipped at RT or on wet ice. Note most dry pellets the
    JGI has received will not resuspend.

> *DNA should be shipped to the JGI in **one tube**.* The tube should be
> legibly labeled with

-   Short description of sample,

-   Name of PI on Proposal,

-   Concentration,

-   prepped date, and

-   Name or initials of primary contact (primary contact indicated in
    "JGI Required Information" form).

> If the DNA prepared in multiple preps, each prep should be QC'ed
> separately, and good preps pooled into one tube for shipping to the
> JGI.
>
> **Please Note:** JGI procedures such as (CTAB) for isolating
> prokaryotic HMW gDNA and various eukaryotic HMW protocols are
> available on the following website:
> http://my.jgi.doe.gov/general/index.html
>
> Elution of genomic DNA from Qiagen columns often yields DNA that is
> sheared to a MW of \~ 20KB and is therefore not recommended for whole
> genome shotgun sequencing projects.
>
> Beware of poor quality enzymes as they are sometimes contaminated with
> genomic DNA from enzyme source microbes.

**Quality control-gel electrophoresis conditions:**

http://my.jgi.doe.gov/general/index.html

To determine MW, mass and concentration, run a 0.75 - 1% agarose gel at
1-3 v/cm for 3 hrs - overnight, using the narrowest comb available. Use
lambda / Hind III markers and mass standards (mass standards can be
lambda markers if they are quantified, although dilutions of uncut
lambda are probably best). The gDNA should be \> 23 KB lambda marker
with some gDNA held up in the well. Smearing below the 23 KB marker is
bad. RNA blobs are bad. *A picture of this gel should be emailed to the
JGI contacts prior to shipment of the DNA*. **A standards kit is
available upon request.**

+-----------------------------------+----------------------------------+
| > ![](media/image1.               | > ![](media/image2.              |
| png){width="2.4270833333333335in" | pct){width="2.292361111111111in" |
| > height="5.222222222222222in"}   | > height="5.1722222222222225in"} |
| >                                 | >                                |
| > Good gDNA prep                  | > Bad gDNA preps                 |
+-----------------------------------+----------------------------------+

You are ready for the next step:
[http://my.jgi.doe.gov/general/*gettingstarted.html*](../%20http://my.jgi.doe.gov/general/gettingstarted.html)

Step 3: Required Information Spreadsheets.