Difference between revisions of "Sequencing"

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= TECHNOLOGY =
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|title=Sequencing Service
 
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The GTC offers Next-Generation sequencing on the Illumina's NovaSeq and Element Bioscience's AVITI platform. More details on the [[Pricing| pricing]] page.
  
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We also have Nanopore PS2 solo for long read sequencing.
  
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= LIBRARY PREP SERVICE =
  
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= Technology =
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We offer many options for library prep for a wide range of applications and input levels down to RNA from single cells. Please refer to the pricing page for more information.
  
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The GTC offers Next-Generation sequencing on the Illumina platform. We have two GAII systems and one HiSeq2000. The GAII systems typically yield 10-30 million reads per lane in single read or paired end mode. The HiSeq2000 typically yields 70-100 million reads per lane for only about 50% higher costs. Further costs savings can be realized with sample multiplexing.
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= PRICING =
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= Library Prep Services =
 
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We offer three full service options for library prep each using the Illumina TruSeq system with up to 12 unique barcodes for multiplexing. The Manual library prep protocol yields the highest quality libraries and is compatible with low sample inputs for applications like ChIP-seq. The SPRIworks protocol uses the SPRIworks system from Beckman for high-throughput processing and is appropriate for preparing libraries from high quality and quantity DNA inputs. The RNA-seq protocol is a manual protocol starting from total RNA and uses the Illumina TruSeq RNA kit.
 
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= Pricing =
 
  
 
For pricing information - [[Pricing| Click Here]]
 
For pricing information - [[Pricing| Click Here]]
  
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= Sample Submission Guidelines =
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{{SeqSubmissionGuide}}
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Please use our sample submission forms found [[Forms|here]].
 
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Users may submit fully prepared libraries with Illumina adapters or dsDNA or total RNA for our library prep services.
 
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User prepared libraries should be gel-purified and provided UNDILUTED in EB or similar. Please submit 10uL of undiluted sample. We will determine the concentration by RT-PCR and make the appropriate dilutions. Excess sample will be retained in our freezers for potential future re-run. Users are also strongly encouraged to retain a portion of their samples in case of emergency.
 
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For the library prep service please submit dsDNA for the standard protocols or total RNA for the RNA-seq protocol. We will provide all reagents for adapter ligation and enrichment. There is a wide range of suitable volumes and concentrations but we will need to know approximate values.
 
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GTC will provide sequencing primers for libraries prepared with standard Illumina adapters. If custom sequencing primers are required they must be provided at the time of sample submission.
 
  
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= Data =
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= DATA =
  
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Images acquired from the sequencer are processed through the bundled Illumina image extraction pipeline to get the sequence and quality score for each base. If requested, the reads can be aligned to a reference genome using the Illumina ELAND algorithm. An in-depth QC report is included in the package.
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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 - [[SequencingQC|Sequencing]]
 
* QC Details - [[SequencingQC|Sequencing]]
 
* Formats Details - [[SequencingFormats|Sequencing]]
 
* Formats Details - [[SequencingFormats|Sequencing]]
  
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== Turnaround Time ==
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== TURNAROUND TIME ==
  
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Each sequencer processes 8 samples per run, or 7 samples plus a control. Full flowcell submissions (7 samples) can usually be started within one week of submission. Partial submissions of less than seven samples are put into a project queue where they join existing samples or await others before processing. Wait times for partial submissions vary but are generally two weeks or less until the START of the run depending on the requested run configuration and demand from other users. The most common run configuration is short (40 bases) and single read. Longer read and paired-end samples may take longer to turn around as there are generally fewer similar samples in the queue to fill out runs. Once a run has started, estimate approximately 1 day per 20 bases for the run and an additional 24-48 hours for data processing. Samples requiring library prep will also take an additional approximately one week for the prep.
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2-3 weeks
  
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= Applications =
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= 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.
 
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.

Latest revision as of 16:51, 10 July 2024

TECHNOLOGY

The GTC offers Next-Generation sequencing on the Illumina's NovaSeq and Element Bioscience's AVITI platform. More details on the pricing page.

We also have Nanopore PS2 solo for long read sequencing.

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. Please refer to the pricing page for more information.

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

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.

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