Field Definitions:

Sample ID	A name, number or code that uniquely identifies this sample.  Only alphanumeric characters, dots, hyphens, and underscores are allowed.
Stock Number	If your sample was drawn from a stock population, this field should uniquely identify that population.  For example, samples extracted from seed should be accompanied by their seed lot number, if known.  Only alphanumeric characters, dots, hyphens, and underscores are allowed.  Maximum 255 characters.
Source Lab	The name of the laboratory from which the samples were submitted.  For example,	Buckler Laboratory or New York State Agricultural Experiment Station.  Only alphanumeric characters, dots, hyphens, and underscores are allowed.  Maximum 255 characters.
Pedigree	A name, number or code that represents the pedigree of the sample.  For example, [CML445/CML176].  Any ASCII character is allowed.
Kingdom	The biological kingdom of the sample.  For example, Plantae for the species Zea mays subsp. mays var. japonica.  Only letters, dots and hyphens are allowed.
Phylum	The phylum of the sample.  Only letters, dots and hyphens are allowed.
Class	The taxonomic class of the sample.  Only letters, dots and hyphens are allowed.
Order	The taxonomic order of the sample.  Only letters, dots and hyphens are allowed.
Family	The taxonomic family of the sample.  For example, Zea for the species Zea mays subsp. mays var. japonica.  Only letters, dots and hyphens are allowed.
Genus	The genus name of the sample.  For example, Zea for the species Zea mays subsp. mays var. japonica.  Only letters, dots and hyphens are allowed.
Species		The species name of the sample.  For example, mays for the species Zea mays subsp. mays var. japonica.  Only letters, dots and hyphens are allowed.
Subspecies	The subspecies name of the sample.  For example, mays for the species Zea mays subsp. mays var. japonica.  Only letters, dots and hyphens are allowed.
Variety	The variety name of the sample.  For example, japonica for the species Zea mays subsp. mays var. japonica.  Only letters, dots and hyphens are allowed.
Population	The name of a specific population from which your sample was drawn.  For example, 2010 increase ears.  Only letters, numbers, dots, hyphens and underscores are allowed.  Maximum 255 characters.
Common Name	The common name of the sample organism.  For example, Silver Queen.
Concentration	The concentration of DNA in the sample, in nanograms per microliter.  For example, .66 for 100 nanograms of DNA in 150 microliters of liquid.  Only numbers and an optional decimal point are allowed.
Volume	The volume of liquid in your sample, in microliters.  For example, 150 for a microplate well three-quarters full.  Only numbers and an optional decimal point are allowed.
Well	The microplate well that contains the sample.  This should be a letter from A-P, followed by a number from 1-24.  For example, B9.
Preparer	The name of the researcher or staff member that prepared the samples.  For example, if a plate is prepared by technician Tim Nguyen as part of research by postdoc Adam Black, the preparer's name is Tim Nguyen.  Only letters, dots and hyphens are allowed.
Plate Name	A name, number or code that uniquely identifies the plate containing the sample, if one exists.  This may be either a serial number supplied by the manufacturer, or a plate number assigned by the researcher.  Only alphanumeric characters, dots, hyphens, or underscores are allowed.  Maximum 50 characters.
Project Name	A name assigned by the researcher that identifies the research project or experiment for which this plate was used.  Only letters, numbers, dots, hyphens or underscores are allowed.  Maximum 255 characters.
Gel Image	Samples should be gel filtered, and an image of the gel included with each submission.  This allows us to judge the quality of your sample DNA and library prep.  Gel images are uploaded simultaneously with sample data through the form on this page.
Location Name	The common name of the specific location from which the sample was obtained.  For example, Field B7.  Only letters, numbers, dots, hyphens or underscores are allowed.
Country		The ISO three-letter code for the country from which the sample was obtained.  For example usa for the United States of America.  
State or Province	The largest sub-national province from which the sample was obtained.  For example, New York.  Only letters, dots and hyphens allowed.
City	The name of the city or town from which the sample was obtained.  For example, Aurora.  Only letters, dots and hyphens allowed.
Elevation	The elevation at which the sample was obtained, in meters above sea level.  Only numbers allowed, with an optional decimal point and sign (+/-).
Latitude		The latitude at which the sample was obtained, in degrees.  North latitude is positive; South latitude is negative.  For example, 42.753961 specifies 42.753961 degrees North latitude.  Only numbers allowed, with an optional decimal point and sign (+/-).
Longitude	The longitude at which the sample was obtained, in degrees.  West longitude is negative; East longitude is positive.  For example, -76.70245 specifies 76.70245 degrees west longitude.  Only numbers allowed, with an optional decimal point and sign (+/-).


Home Page Text:

Institute for Genomic Diversity DNA Sample Tracking Database

This website was designed to streamline the process of submitting multiple DNA samples for genotyping-by-sequencing. Users of the genotyping service should upload a document containing information about their samples, such as pedigree and collection location. This information is stored in combination with the sequencing results to make collaborations (or reuse of data) possible. To begin, click one of the links above to log in or create a new account. 

Guidelines for Genomic DNA Submission

The success of genotyping by sequencing (GBS) is largely determined by DNA quality (molecular weight and purity) and quantity. Below are the guidelines for submitting DNA samples. If you cannot meet the specifications or have questions or concerns, please contact your project manager at jim@spaghettilogic.org.

Quality:

The starting DNA should be free of contaminants and/or symbionts, and should have < 5% organelle DNA if possible. RNA blobs and discrete bands require clean-up; please refer to our recommended RNAse I clean-up protocol. In some cases, the presence of impurities such as polysaccharides or proteins can be predicted by examining the way DNA fragments migrate in an agarose gel. If most of the DNA fragments form a streaky pattern or get stuck on top of the wells, the level of impurities contamination may cause problems in the digestibility of the DNA.
Molecular weight

We believe that high molecular weight DNA will give a better chance of constructing a high quality library. We will not generally accept samples in which most DNA fragments are smaller than 20Kb in size or heavily degraded.

Quantity:

We request 1 ug of DNA at 100 ng/ul. The concentration of the DNA must be >= 50 ng/ul as judged by agarose gel / mass standards or intercalating dye. Please contact your project manager at jim@spaghettilogic.org if you do not have enough material.

Shipping:

Prior to shipping samples to IGD, the collaborator sample information form must be completed and submitted on-line. A well-labeled gel image of your DNA prep is required as part of the submission. This gel should include uncut DNA, DNA cut by HindIII, and HindIII ladder. See a sample gel image . Gel images that do not contain the appropriate size and mass standards will not be approved for shipping.

Shipping Conditions

In order of preference: 
Resuspended in TE (10 mM Tris, ph 7.5 - 8, EDTA 0.1 mM) at >= 50 ng/ul, and shipped on dry ice.
Resuspended in TE (10 mM Tris, ph 7.5 - 8, EDTA 0.1 mM) at >= 50 ng/ul, and shipped on frozen gel packs.
DNA should be shipped in a plate. The plate should be legibly labeled with date, plate name and project number (this will be provided after the sample has been approved for shipping).


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