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History of the DNA Resource Core

DNA Sequencing

The DNA Resource Core started in the spring of 1999 as a direct result of the planning processes for the DF/HCC and was originally called the High-Throughput DNA Sequencing Core. The Executive Planning Committee recognized a growing need in the community for DNA sequencing at a cost that was affordable for academic research labs. The Core became one of the first facilities in the world to obtain an ABI 3700 automated capillary sequencing instrument and began processing samples by the fall of 1999. The Core was fully operational by the spring of 2000 and received funding from the DF/HCC grant in July of that year. In 2001, the Core obtained a second ABI 3700 automated sequencing instrument, enabling the Core to both increase capacity and limit down-time that had occurred during equipment maintenance and repair. In 2006, the Core retired its ABI 3700 instruments and obtained two ABI 3730xl's, which are operating near capacity now.

Over the past eight years, the Core has continued to grow and support the DF/HCC and Harvard community with attention to user-friendly service and quality control, and the Core currently provides outstanding DNA sequencing services at the lowest cost for a DNA sequencing center in the Boston area (with discounts for DF/HCC Members). Currently, the Core sequences close to 200,000 samples per year and is serving over 5000 users in 530 different laboratories both within the DF/HCC community and at other institutions, including MIT and the Whitehead Institute.

PlasmID Repository

In spring 2004, plasmid repository services were added to the DNA Resource Core to reduce the burden on individual labs to store, maintain and distribute plasmid clones and supporting information. To store these plasmids the DNA Resource Core purchased an automated sample retrieval system. This unique robotic system allows storage of 160,000 clones at 80°C in specialized plates that contain 96 individual, 2D-barcoded tubes. The associated software tracks specific clones and their barcodes within the system and manages a picking unit that can retrieve any desired set of clones from their specific plates. By managing the clones in individual tubes instead of standard 96-well plates, this avoids the need to thaw an entire 96-well plate in order to retrieve a single clone. The Core is the first academic center worldwide to employ this state-of-the-art equipment.

The PlasmID repository currently contains over 270,000 plasmids, including collections produced by the Harvard Institute of Proteomics, the Human ORFeome Consortium, as well as plasmids deposited by individual researchers. The Core has also recently acquired the The RNAi Collection (TRC), which contains over 150,000 shRNAs, are now being distributed to researchers at Harvard University and its affiliates. Besides storage of these plasmids in a state of the art automated freezer system, we also maintain a database containing detailed annotation of each plasmid that can be accessed by users through our website. In 2007, the PlasmID repository filled 500 requests for over 4,800 plasmids from researchers around the world. In 2008, the ability to purchase plasmids online using a credit card has been added to our services, a feature we also added for the sequencing services in 2009.

 

The DNA Resource Core offers the following core services

1. DNA Sequencing Service Highlights

  • Sample preparation from glycerol stocks or bacteria pellets
  • Sequencing with user-supplied or free core-supplied primers
  • Turn around time of 24 hours from sample arrival to result download for next day sequencing
  • Same day sequenicng: no more than eight hours of turn around time from sample arrival to data retrieval
  • No charge for re-runs of failed sequencing reactions to test for potential sequencing problems originating at the facility
  • Competitive prices with discounts for DF/HCC members
  • Sequence data and quality reports available on secure website
  • New users are always welcome and special pricing is available for large batch orders.

For more information about our services click here.
To begin sequencing visit the Login Page to learn how to set up an account and log in.


2. Plasmid Clone Service Highlights

  • Storage and distribution of plasmid clones
  • DNA sequencing of deposited plasmids
  • Searchable database of plasmid information
  • Automated system to store clones with standard procedures for quality control
  • Assistance with MTAs, including our expedited MTA process
  • Searching our database and storing clones are free
  • Competitive prices for clone purchases with discounts for DF/HCC members

For more information visit our website PlasmID for information on how to deposit or order clones.


If you're uncertain whether you are part of a DF/HCC member laboratory, please click here to learn about the center and membership, or to search the member directory.

Although we are funded as a DF/HCC Core, our services are open to the entire scientific community.

 

Meet the Staff of the DNA Resource Core

Name Position Phone Email
Wade Harper, PhD Director TBA

wade_harper@hms.harvard.edu

Glenn Beeman, MA PlasmID Platform Manager (617)432-7708 glenn_beeman@hms.harvard.edu
Ashkan Bigdeli Bioinformatics Coordinator (617)432-7708 ashkan_bigdeli@hms.harvard.edu
Li Chan, MA Operations Director (617) 432-7708 li_chan@hms.harvard.edu
Francis Farley, PhD Research Assistant: DNA Sequencing (617) 432-7708 francis_farley@hms.harvard.edu
Yili Li Research Assistant: DNA Sequencing (617) 432-7708 yili_li@hms.harvard.edu
Zhenwei Shi Research Assistant: DNA Sequencing (617) 432-7708 zhenwei_shi@hms.harvard.edu
William Veguilla Research Assistant: PlasmID Repository (617) 432-7708 william_veguilla@hms.harvard.edu
Jenna Weinstein Research Assistant: PlasmID Repository (617) 432-7708 jenna_weinstein@hms.harvard.edu

 

The DNA Resource Core Facilities

The DNA Resource Core is located in the LHRRB building at 240 Longwood Avenue at the Harvard Medical School in Boston, MA. The facility is committed to implementing automation to increase throughput and facilitate quality control in all aspects of core services.

ABI 3730

The DNA Sequencing core has two 48-capillary ABI 3730 DNA Analyzers.

ABI_3730

 

Biomek NX

This state of the art liquid handling robot is fully integrated into the DNA sequencing process by handling DNA cleanups after sequencing reactions in a 96-well format.

NX

 

The Biobank

This automated storage system holds 160,000 different samples at -80°C. Each sample is in an individual tube with a unique 2-D barcode on the bottom, which is tracked by our online PlasmID database.

biobank2

 

Funding for the DNA Resource Core

 

Harvard Medical School  

The Core is hosted by the Department of Biological Chemistry & Molecular Pharmacology at Harvard Medical School which is located in the Longwood Medical Area in Boston.

 
Dana Farber Harvard Cancer Center  

The Dana-Farber Cancer Center (DF/HCC) DNA Resource core is one of many core facilities created to support researchers within the Cancer center. Cores are central laboratories, each capable of performing a specific set of experimental functions that enable DF/HCC investigators to perform experiments faster, more accurately and at an affordable price. For more information about the Dana-Farber/Harvard Cancer Center or other DF/HCC core facilities, programs, and members, please click here.

 

To acknowledge sequencing work done at the DNA Resource Core in your publications, please follow this format:

Sequencing reactions were carried out with an ABI3730xl DNA analyzer at the DNA Resource Core of Dana-Farber/Harvard Cancer Center (funded in part by NCI Cancer Center support grant 2P30CA006516-48).

 

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