Sequencing

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Sequencing Service
Dna seq.jpg


TECHNOLOGY

The GTC offers Next-Generation sequencing on the Illumina platform. We have 3 HiSeq 2500 systems with Rapid mode capabilities.

There are two options for Illumina sequencing. HiSeq "Standard" and HiSeq "Rapid". More details on the pricing page.


LIBRARY PREP SERVICE

We offer many options for library prep for a wide range of applications and input levels down to RNA from single cells. The following chart can be used as a starting point but you should feel free to consult GTC staff about which prep is right for you.


Sample Type Application Input amount (ng)** Prep
Genomic DNA Any >100 TruSeq DNA
ChIP Any 1-100 TruSeq ChIP
RNA (total) Basic (PolyA) Expression >100 TruSeq Stranded RNA
RNA (total) With Ribozomal Deletion 100-4,000 TruSeq Stranded RNA with RiboZero
RNA (total) Ultra Low Input <10 Clonetech UltraLow Input

PRICING

For pricing information - Click Here

SEQUENCING SUBMISSION GUIDELINES

You can download detailed guidelines in word format from here.

STEP 1: REGISTRATION (FOR NEW CUSTOMERS ONLY)

  • INTERNAL CUSTOMERS: Please click here to register in our system.
  • EXTERNAL CUSTOMERS: Fill out a new customer form (Available Here) with billing information. Once the form is emailed to us, we will register you in our database and notify you when you can submit samples to us.

All external customers please obtain a purchase order number prior to your submission. If you need a quote, please email us at wibr-genome@wi.mit.edu or call us at 617-258-8803. Blanket purchase orders are preferred, if you plan to submit multiple projects over time.


STEP 2: PREPARATION OF SAMPLES

SUBMISSION OF SAMPLES FOR LIBRARY PREPARATION

Samples should be in a buffer that does not contain trace amounts of phenol or EDTA. We will save and return any unused input material after libraries are successfully prepared.

Below are our input requirements for Library Prep Service

Sample Type Sonication/Fragmentation* Fragment Size (bp) Input requirements (ng)** Volume (ul)
Genomic Required 200 to 400 500 to 1000 10-50
ChIP Required Variable (specify) 10 to 50 10-40
RNA (total) NA NA 100 to 1000 10-50

*Unless special arrangements are made with us in advance, we will assume that your genomic DNA sample has been fragmented, by sonication or otherwise, prior to submission.

**We can work with less if necessary, but it is best if you elute your DNA in 50 ul or less if you believe we may need to use all of it. Please give us at least 10uL of sample to ensure we have enough for QC and prep.

SUBMISSION OF PRE-PREPARED LIBRARIES

We typically need 10-20 ul of each library at 5 ng/ul or greater. If your library is less concentrated than 5 ng/ul, we’ll quantify it to make sure we have enough to sequence.


STEP 3: ONLINE SUBMISSION OF SEQUENCING LIBRARIES

  • Please complete the online submission form (Link To Form Available Here). Questions or problems related to the submission should be directed to Sumeet Gupta at sgupta@wi.mit.edu
  • Every physical sample tube should have its own Genome Tech Core ID (GTC ID) number (automatically generated and emailed to you immediately after submission of the online form), even if you plan to multiplex them.
  • Please write your name GTC ID numbers on the tubes. We prefer 1.5 ml tubes.


STEP 4: DROP-OFF OR SHIPPING

When you are ready, you may hand deliver or ship samples them on dry ice to:

Whitehead Institute Genome Technology Core
455 Main Street, Room 325
Cambridge, MA 02142

Please do not ship without first contacting someone in the lab, to make sure that we are here to receive your package. Do not rely on voicemail. Please wait until you hear back from someone.

DATA

Images acquired from the sequencer are processed through the bundled Illumina image extraction pipeline to get the sequence and quality score for each base. An in-depth QC report is included in the package.

TURNAROUND TIME

2-3 weeks

APPLICATIONS

Next-Generation Sequencing can be used for a wide variety of applications including ChIP-Seq, RNA-Seq, smallRNA-seq, GWAS and much more. Visit Illumina's web site or contact us to discuss your project goals.