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Next-generation sequencing service

eagle-i ID

http://harvard.eagle-i.net/i/0000012c-bd01-ba44-02c0-2b6880000000

Resource Type

  1. Material analysis service

Properties

  1. Fee for service
    Yes
  2. Resource Description
    "The Next-Gen Sequencing Facility is currently preparing SOLiD instrument runs for full slides on fragment libraries. Fragment libraries include whole genome resequencing, targeted resequencing (using Agilent SureSelect technology), RNA-seq, ChIP-seq, and small RNA libraries. Customers may create their own libraries after project consultation with the Core and submit them for quantitation and processing. Library preparation is also available in the Core for whole genome, whole transcriptome, and small RNA fragment libraries. A full slide instrument run consists of all post-library construction processing through to providing sequence data as follows. The Core performs a quantitative PCR (qPCR) assay on every library to determine its concentration. Using the information from the qPCR, the Core performs a series of emulsion PCRs (ePCR) to amplify template onto beads with individual fragments from the library (or pool of bar-coded libraries). At this stage a spike-in control library is added for processing validation once the run is complete. The completed ePCR then undergoes a breaking and enrichment procedure to release the templated beads from the oil mixture and to enrich for the templated beads that will be deposited onto slides to run in the SOLiD instrument. Before a full run is conducted in the SOLiD, a quality control run is performed to ensure that the ePCR and breaking worked properly. Once the beads pass the QC run, a full slide run is performed on the instrument. Upon completion, each customer is provided with the color space sequence data and run quality data. The Core will keep a record of this data as well as the raw intensity files in permanent electronic records, however the intensity files are not necessary for downstream analysis. All image data is discarded once the sequence run alignment is confirmed by analyzing our spike-in control library data. As of July 2009, the MGCF has teamed up with Geospiza to offer SOLiD sequencing bioinformatics support through their GeneSifter on-line application. Use of this software is included in the cost of an instrument run for up to three months after data is posted. This software allows users to perform alignments to their reference species as well as perform downstream data analysis. Currently, analysis pipelines are available for RNA-seq, Digital Gene Expression, genomic resequencing and small RNA SOLiD sequencing runs, but many more analysis pipelines are under construction and will be available soon. For more information about using the GeneSifter application through the Next-Gen Sequencing Facility, please email nextgen@iddrc.org." Service provided by the Next-Gen Sequencing Sub-Facility.
  3. Service Fee URL
    http://core.iddrc.org/molecular-genetics/?page_id=10#Pricing
  4. Related Resource
    ABI SOLiD 4 sequencing system
  5. Service Provided by
    Molecular Genetics Core Facility (BCH)
  6. Website(s)
    http://core.iddrc.org/molecular-genetics/?page_id=10
  7. Related Technique
    Next generation DNA sequencing
 
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Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016