Guidelines for submission of Shotgun Libraries to the DOE Joint Genome
Institute

> **Library quality is the most critical component in the success of
> sequencing projects. Users may send libraries constructed in their lab
> in the following formats by order of preference: transformation stock,
> 384-well nunc plates, or ligation. The JGI only sequences in both
> directions. We cannot sequence fewer than 20 plates for libraries not
> in standard JGI vectors (pUC18, pMCL200 and pCC1Fos).**
>
> **If you cannot meet the JGI specifications for whole genome shotgun
> libraries or have questions or concerns, please contact
> jgi_project_management@lanl.gov and your project manager.**

**[JGI User Supplied Library Specifications: Transformation
Stock]{.underline}**

-   Must by accompanied by vector information. (please see required
    vector information at the bottom of this document)

-   Must by accompanied by a completely filled out
    RI_Shotgun_Libraries.xls document detailing construction & QC
    protocols for the library.

-   Must be test transformed by the user, and the number of colony
    forming units/ul reported, as well as the total volume provided.

-   Must have \< 10% insertless rate as measured by QC'ing at least 24
    clones.

-   Must have an efficiency of 1.7xs the desired number of clones to be
    end sequenced. QPixes only pick \~60% of white colonies.

-   A representative gel image used to verify insert must be submitted.

-   Inserts must be contained in white colonies. (we do not pick blue
    colonies)

-   Must be shipped on dry ice.

**[JGI User Supplied Library Specifications: 384 well Nunc
Plates]{.underline}**

-   Must be 384-well Nunc plate with lid (Tissue Culture Treated,
    Sterile) is P/N Beckman: #164688 for the plates and 538619 for the
    seals. CIC sells the same seals, the part number is FS-100.

-   Must by accompanied by vector information. (please see required
    vector information at the bottom of this document)

-   Must by accompanied by a completely filled out
    RI_Shotgun_Libraries.xls document detailing construction & QC
    protocols for the library.

-   Must provide the OD of each well in separate document and identify
    blank wells.

-   We will not copy or rearray plates. We will ship plates back to
    user.

-   Must be shipped on dry ice. We recommend sealing the plates and
    using lids, and if shipping more than one plate, securing them with
    a rubber band.

**[JGI User Supplied Library Specifications: Ligation
Stock]{.underline}**

-   Must by accompanied by vector information. (please see required
    vector information at the bottom of this document)

-   Must by accompanied by a completely filled out
    RI_Shotgun_Libraries.xls document detailing construction & QC
    protocols for the library.

-   Must be test transformed by the user, and the number of colony
    forming units/ul reported, as well as the total volume provided.

-   Must have \< 10% insertless rate as measured by QC'ing at least 24
    clones.

-   Must have an efficiency of 1.7xs the desired number of clones to be
    end sequenced. QPixes only pick \~60% of white colonies.

-   A representative gel image used to verify insert must be submitted.

-   Inserts must be contained in white colonies. (we do not pick blue
    colonies)

-   Must be shipped on wet or dry ice.

**[JGI User Supplied Library Specifications: Vector
Information]{.underline}**

-   The following information must be provided for all vectors:

    -   Vector name

    -   Vector sequence

    -   Vector source

    -   Vector Accession Number

    -   Complete sequence of any adaptors

    -   Sequencing Primer Names

    -   Sequencing Primer Sequences

    -   Antibiotic

    -   Antibiotic concentration

    -   Cloning site (cut site)

    -   Other CDS/features.

-   The JGI does not stock and cannot process libraries requiring growth
    or selection on gentamycin or tetracycline.

**[JGI User Supplied Library Specifications: Shipping]{.underline}**

> *Prior to shipping samples to the JGI, the library prep must first be
> reviewed & approved. Complete the appropriate RI
> (<http://my.jgi.doe.gov/general/gettingstarted.html> and email it
> along with a well-labeled gel image of your library QC to your project
> manager.*
>
> *Transformation and Ligation Stocks should be shipped to the JGI in
> **one tube per library**.*
>
> The tube should be legibly labeled with

-   Short description of sample or genus, species, strain,

-   Name of PI on Proposal,

-   Number of colonies per microliter (cfu),

-   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.
>
> *Plates* must be shipped on dry ice. We recommend sealing the plates
> and using lids, and if shipping more than one plate, securing them
> with a rubber band.

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

Step 3: Required Information Spreadsheets.