Next-Generation Sequencing

NEXT GENERATION SEQUENCING SERVICES PRICING AND ORDERING

You can check our prices and place an order for our Next-Generation Sequencing services (including library prep) using our Laboratory Information Management System (LIMS), DUGSIM: Duke University Genome Sequencing Information Manager. At any stage in DUGSIM, you can hover over the help icon ? in order to get more details. You can also track your existing order status with our online order tracker or by contacting us at sequencing@duke.edu.

Start DUGSIM  

If you have any project design or technical questions, you can contact us by email or schedule a phone/in-person consultation:

Go to:

❯ Sample Requirements
❯ Ordering Guidelines


SAMPLE REQUIREMENTS

Illumina equipment Illumina HISEQ AND MISEQ

Samples must be resuspended in nuclease-free water. Samples should be submitted in a 1.5ml tube clearly marked with your initials followed by a 2- to 3- digit identifier. Your order number should be marked on the side of the tube. See input amount in the table below. Note that if you use Nanodrop, your DNA concentration is often over-estimated (~3x).

Library TypeInput TypeConcentrationVolume
DNA-Seqgenomic DNA40 ng/µl50 µl
">mRNA-Seqtotal RNA20 ng/µl50 µl
RNA-Seqtotal RNA20 ng/µl50 µl
Low RNA input RNA-Seqtotal RNA1 ng/µl10 µl
smRNA-Seqtotal RNA200 ng/µl15 µl
Mate-Pairgenomic DNA200 ng/µl50 µl
Exome Capturegenomic DNA40 ng/µl50 µl
RAD-Seqgenomic DNA40 ng/µl50 µl
ChIP-SeqChIP enriched DNA1 ng/µl30 µl

If you submit your own libraries, concentration should be >10nM in more than 15μl; EB (Tris-Cl 10mM, pH 8.5).

PacBio equipment PacBio RS II

The PacBio template preparation process does not utilize amplification techniques; therefore, the input DNA quality will be directly reflected in the sequencing results. Any DNA damage (e.g., basic sites, nicks, interstrand crosslinks) or contaminants (e.g., single-stranded DNA, RNA, proteins, dyes, or salts, phenol) present in the input material will impair performance of the system. PacBio recommends Qiagen gDNA extraction kits. Do not submit home-brew extractions. Please indicate your protocol when you submit your sample. gDNA samples need an OD 260/280 ratio of approximatively 1.8 to 2. For PCR products, gel cuts may be done, but not if the gel has been exposed to ethidium bromide. PCR products must be either cleaned prior to submission.

Library Insert SizeInput TypeAmountVolume
500-800bpPCR productµg<150 µl
800bp-4kbPCR or RTPCR product1-4 µg<150 µl
15-20kbgenomic DNA>15 µg<150 µl

Ensure that your DNA sample:

  • Is double-stranded. Single-stranded DNA will not be made into a SMRTbell template and can interfere with quantitation and polymerase binding.
  • Has undergone a minimum of freeze-thaw cycles.
  • Has not been exposed to high T (>65°C for 1 h can cause a detectable decrease in sequence quality).
  • Has not been exposed to pH extremes (<6 or >9).
  • Does not contain insoluble material, and is not colored or cloudy.
  • Does not contain RNA.
  • Has not been exposed to intercalating fluorescent dyes or UV radiation.
  • Does not contain chelating agents (e.g., EDTA), divalent metal cations (like Mg 2+), denaturants (like guanidinium salts, phenol), or detergents (like SDS, Triton-X100).
  • Does not contain carryover contamination from the starting organism/tissue (like heme, humic acid, polyphenols).

ORDERING Guidelines

Estimate the cost of a project

1. Click on "Estimate cost".
2. If you have multiple affiliations, select the appropriate one.
3. Choose your sequencing platform, library preparation type + quantity, and sequencing protocol + quantity.
4. Validate your estimate request by clicking on "Estimate cost".
5. If you have any questions, you can send a message to our staff using the comment box located below the cost estimate.

Create an account in DUGSIM

1. Go to DUGSIM.
2. Click on "Sign up".
3. Enter your name, your email (this will be your login), and your password.
4. Choose an institution from the dropdown list or create a new one.
5. Join an existing lab (designated account manager will receive your request) or create a new lab (you will become the account manager for this lab).

Getting an official quote (ACCOUNT REQUIRED)

1. Prepare a cost estimate as described above.
2. Sign in DUGSIM if not already.
3. Click on the "Request quote" button at the bottom of the "Estimate the cost of a project" page.
4. Someone from our staff will review and process your request within a few hours.

Placing an order (quote required)

1. Once your quote is approved, you will receive an email from DUGSIM.
2. Sign in DUGSIM if not already.
3. Go to the "Main" page and locate your quote.
4. For non-Duke users: fill and approved the online authorization form then click on "Advance to Orderable"; Duke users can directly place an order from the aproved quote.

Submit your sample(s) (order required)

1. Once your order is placed and we have validated your mode of payment (reception of your Purchase Order form or valid Fund Code), your project will be assigned a unique order number and you will be able to submit your sample.
2. Once you are ready to submit your samples, make sure to go to log back into your DUGSIM account, go to your order and click on the "Edit samples etc." button. A table will appear for you to fill in information about your samples.  All samples should be accompanied by both a copy of your order (printed from DUGSIM).

3. If you are on campus, please bring your samples/libraries to Heather Hemric, ZhengZheng Wei, or Holly Dressman in:

CIEMAS, room 2208B. 
101 Science dr.

Sample Drop-Off Hours at CIEMAS 2208B:

  • Monday – Friday: 10 -11 A.M.
  • Monday – Friday: 2 – 3 P.M.

4. Starting August 1st 2017, Samples can also be dropped off anytime during week days at the Chesterfield Building downtown Durham:

701 W. Main Street,
Suite 320

5. For non-Duke researchers, send yoursamples to this shipping address: 

Att: [TECHNOLOGY] sequencing  (replace [TECHNOLOGY] by "Illumina" or  "PacBio")
GCB Sequencing and Genomic Technologies Shared Resource
Chesterfield Bldg.,
Duke University,
701 W. Main Street,
Suite 320,
Durham, NC 27701
USA