Service Request Workflow

GETTING STARTED:
What you need to do

CORE OPERATING PROCEDURES:

FINISHING UP:

TIP: click on the orange buttons to expand (or close) each section in the workflow.

(Epi)Genetic Profiling Services

Overview

  • The core accepts both samples that require library preparation and sequencing as well as libraries ready for sequencing. In both cases, there will be a quality control step prior to agreement of service. The core does not accept library preparation only requests.
  • Libraries with bias in base composition or with a low diversity base composition will generate poor sequence quality runs. Please inform us if you are submitting such libraries [MORE]
  • Please refer to specific services using the menu on the left for detailed quality control descriptions.
  • The price for library preparation is per library, and includes sample quality control, library preparation and library validation.
  • The price for sequencing is per lane, and includes de-multiplexing (if required), alignment if available and requested and two years data storage. For methylation sequencing services, methylation calls are also provided with alignments.
  • Sequencing is performed on HiSeq 2500 or MiSeq Illumina instruments.
  • Sequencing output is heavily dependent on the quality of library preparation. When you submit libraries for the first time, please contact us to discuss the quality of your libraries and the concentration at which you would like them to be loaded on the sequencer.
  • Libraries made by the core, routinely yield clusters between 750-800 k/mm2 passing the illumina chastity filter. We cannot guarantee similar clustering and/or quality for libraries made by customers of the core.
  • We require that core clients acknowledge the Epigenomics Core of Weill Cornell Medical College in publications and presentions enabled by Epigenomics core resources.

Sample submission tips

  • To request a sequencing service, please fill out a request in our Agilent Crosslab/iLab Service Request LIMS, and upload the following excel form with the required details Sequencing Sample Submission Form. Please refer to the GETTING STARTED section of our Sample Workflow above for detailed sample submission instructions.
  • The core routinely runs the HiSeq2500 with the following sequencing recipes: single read clustering -50 cycles/bases and pair end clustering 50 cycles/bases. If you require a different read length (or dual indexing), please provide enough samples/libraries for at least 2 sequencing lanes (or multiples thereof).
  • Each sequencing service needs to reflect one type of library preparation and one type of sequencing recipe.
  • Please use the Agilent Crosslab/iLab service ID and the sample number you have indicated in the submission form to label your tubes clearly, tubes without a service ID and sample number will not be accepted.
  • Once samples are submitted and pass quality control, they are entered into a sample or library queue.
  • Please be aware that only libraries using the same sequencing recipe can be run on the same flow cell and all lanes on the flow cell must be filled before the flow cell can be loaded on the sequencer.
  • If you have less than 24 samples to multiplex, the core will multiplex altogether in one pool, and sequence over the required number of lanes. If you have more than 24 samples, you should randomize your samples before listing them on the sample sheet. They will be pooled in the order submitted using a strategy that will minimize batch effect.
  • The MiSeq personal sequencer has a single lane and only supports paired end clustering. [MiSeq PDF]

Timeline:
Approximate time for library preps and sequencing is 4-8 weeks if all samples pass quality control.
Approximate time for data pre-processing and transfer is 1-2 weeks from the end of a successful sequencing run.

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