Difference between revisions of "Sequencing"
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Revision as of 09:31, 30 August 2019
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Contents
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 |
|---|---|---|---|
| ChIP | Any | 1-100 | Swift |
| RNA (total) | Basic (PolyA) Expression | >100 | KAPA Stranded RNA |
| RNA (total) | With Ribozomal Deletion | 100-4,000 | KAPA with RiboZero |
| RNA (total) | Ultra Low Input | <10 | Clonetech UltraLow Input |
PRICING
For pricing information - Click Here
SEQUENCING SUBMISSION GUIDELINES
STEP 1: REGISTRATION (FOR NEW CUSTOMERS ONLY)
- INTERNAL CUSTOMERS: Do NOT require to register in the system
- EXTERNAL CUSTOMERS: Have your lab administrator register in the Whitehead Cores Database - https://cores.wi.mit.edu/.
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) |
|---|---|---|---|---|
| DNA (genomic/ChIP) | Required | Variable | 1 to 500 | 40ul or less |
| RNA (total) | NA | NA | 10 to 1000 | 14ul or less |
*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.
- QC Details - Sequencing
- Formats Details - Sequencing
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.
